diff --git a/cell_type_annotation.md b/cell_type_annotation.md
index 5f8d986..d99b784 100644
--- a/cell_type_annotation.md
+++ b/cell_type_annotation.md
@@ -855,897 +855,7 @@ par(mfrow = c(3,3))
AUCell_exploreThresholds(cell.aucs[10:18], plotHist = TRUE, assign = TRUE)
```
-
-
-``` output
-$`Haematoendothelial progenitors`
-$`Haematoendothelial progenitors`$aucThr
-$`Haematoendothelial progenitors`$aucThr$selected
- R_k3
-0.273
-
-$`Haematoendothelial progenitors`$aucThr$thresholds
- threshold nCells
-Global_k1 0.173 196
-L_k2 0.199 138
-R_k3 0.273 48
-
-$`Haematoendothelial progenitors`$aucThr$comment
-[1] "The global distribution overlaps the partial distributions. "
-
-
-$`Haematoendothelial progenitors`$assignment
- [1] "cell_9963" "cell_11842" "cell_9934" "cell_11154" "cell_10322"
- [6] "cell_11337" "cell_11770" "cell_12021" "cell_11667" "cell_10047"
-[11] "cell_11290" "cell_11733" "cell_11827" "cell_11404" "cell_11511"
-[16] "cell_10146" "cell_10718" "cell_12090" "cell_10715" "cell_10458"
-[21] "cell_10216" "cell_10010" "cell_11760" "cell_10126" "cell_10654"
-[26] "cell_9813" "cell_11916" "cell_12082" "cell_11769" "cell_11484"
-[31] "cell_11414" "cell_11932" "cell_11791" "cell_9974" "cell_11199"
-[36] "cell_10256" "cell_10319" "cell_10977" "cell_10945" "cell_11077"
-[41] "cell_10895" "cell_10168" "cell_9770" "cell_11772" "cell_11771"
-[46] "cell_11611" "cell_11287" "cell_10095"
-
-
-$`Intermediate mesoderm`
-$`Intermediate mesoderm`$aucThr
-$`Intermediate mesoderm`$aucThr$selected
-minimumDens
- 0.0723
-
-$`Intermediate mesoderm`$aucThr$thresholds
- threshold nCells
-outlierOfGlobal 0.4388 0
-Global_k1 0.1984 262
-L_k2 0.2203 168
-R_k3 0.1547 516
-minimumDens 0.0723 841
-
-$`Intermediate mesoderm`$aucThr$comment
-[1] "The AUC might follow a normal distribution (random gene-set?). The global distribution overlaps the partial distributions. "
-
-
-$`Intermediate mesoderm`$assignment
- [1] "cell_11995" "cell_9963" "cell_10910" "cell_11021" "cell_10433"
- [6] "cell_11395" "cell_10779" "cell_10883" "cell_10721" "cell_10116"
- [11] "cell_10785" "cell_11781" "cell_11147" "cell_11842" "cell_11218"
- [16] "cell_11441" "cell_11558" "cell_9979" "cell_10323" "cell_11663"
- [21] "cell_10935" "cell_11567" "cell_10673" "cell_11634" "cell_10815"
- [26] "cell_10077" "cell_9934" "cell_11888" "cell_10356" "cell_10490"
- [31] "cell_9921" "cell_10062" "cell_9809" "cell_11906" "cell_10951"
- [36] "cell_10520" "cell_10142" "cell_12176" "cell_11850" "cell_10284"
- [41] "cell_9781" "cell_11885" "cell_11687" "cell_10523" "cell_11100"
- [46] "cell_10881" "cell_10774" "cell_12107" "cell_11216" "cell_10439"
- [51] "cell_10902" "cell_10856" "cell_11702" "cell_11269" "cell_10248"
- [56] "cell_11883" "cell_11682" "cell_10877" "cell_9933" "cell_10843"
- [61] "cell_11154" "cell_12052" "cell_9895" "cell_12028" "cell_10454"
- [66] "cell_11750" "cell_12059" "cell_10615" "cell_10751" "cell_10387"
- [71] "cell_10245" "cell_11767" "cell_9919" "cell_11976" "cell_11971"
- [76] "cell_10797" "cell_10094" "cell_11724" "cell_11030" "cell_11855"
- [81] "cell_10754" "cell_9905" "cell_11530" "cell_11352" "cell_10357"
- [86] "cell_12074" "cell_12012" "cell_11561" "cell_11398" "cell_12075"
- [91] "cell_12177" "cell_11653" "cell_10644" "cell_11993" "cell_10322"
- [96] "cell_11900" "cell_11315" "cell_10474" "cell_10480" "cell_11220"
-[101] "cell_10440" "cell_11596" "cell_10296" "cell_11337" "cell_11856"
-[106] "cell_11728" "cell_10241" "cell_12016" "cell_11770" "cell_10917"
-[111] "cell_11805" "cell_12002" "cell_10599" "cell_10846" "cell_10687"
-[116] "cell_11330" "cell_11081" "cell_9953" "cell_10181" "cell_10395"
-[121] "cell_12021" "cell_11667" "cell_10547" "cell_11329" "cell_10332"
-[126] "cell_10562" "cell_11183" "cell_11138" "cell_10385" "cell_10125"
-[131] "cell_10047" "cell_10038" "cell_10386" "cell_11673" "cell_10105"
-[136] "cell_12162" "cell_10749" "cell_11549" "cell_11458" "cell_11290"
-[141] "cell_11213" "cell_10849" "cell_11465" "cell_9885" "cell_10416"
-[146] "cell_10847" "cell_11009" "cell_11733" "cell_10756" "cell_10479"
-[151] "cell_11260" "cell_11002" "cell_10117" "cell_10933" "cell_11840"
-[156] "cell_10922" "cell_11495" "cell_11380" "cell_10478" "cell_11026"
-[161] "cell_11880" "cell_11896" "cell_12110" "cell_11115" "cell_10559"
-[166] "cell_12151" "cell_11109" "cell_11014" "cell_11526" "cell_11018"
-[171] "cell_11582" "cell_11476" "cell_10065" "cell_10628" "cell_11603"
-[176] "cell_10825" "cell_9851" "cell_10634" "cell_10791" "cell_9844"
-[181] "cell_10886" "cell_11931" "cell_11975" "cell_11150" "cell_10450"
-[186] "cell_12115" "cell_11506" "cell_11239" "cell_11130" "cell_10011"
-[191] "cell_11922" "cell_11827" "cell_10393" "cell_11982" "cell_10229"
-[196] "cell_12140" "cell_9799" "cell_10907" "cell_11957" "cell_9784"
-[201] "cell_11204" "cell_10292" "cell_11229" "cell_10692" "cell_11370"
-[206] "cell_9972" "cell_10914" "cell_10027" "cell_10262" "cell_11657"
-[211] "cell_11552" "cell_11123" "cell_10900" "cell_11093" "cell_9778"
-[216] "cell_9938" "cell_11001" "cell_11619" "cell_12160" "cell_9876"
-[221] "cell_9776" "cell_10394" "cell_10029" "cell_11377" "cell_11679"
-[226] "cell_11054" "cell_11528" "cell_11913" "cell_11515" "cell_10435"
-[231] "cell_10758" "cell_10220" "cell_10624" "cell_11716" "cell_11371"
-[236] "cell_12042" "cell_10414" "cell_10828" "cell_10659" "cell_11424"
-[241] "cell_11096" "cell_12171" "cell_11803" "cell_11404" "cell_10561"
-[246] "cell_11180" "cell_10046" "cell_10009" "cell_9792" "cell_11853"
-[251] "cell_11095" "cell_11511" "cell_11835" "cell_11463" "cell_10146"
-[256] "cell_10317" "cell_11407" "cell_12173" "cell_10161" "cell_10438"
-[261] "cell_10981" "cell_10079" "cell_11210" "cell_11174" "cell_10876"
-[266] "cell_10087" "cell_11630" "cell_11434" "cell_9888" "cell_10367"
-[271] "cell_11107" "cell_11994" "cell_10192" "cell_11822" "cell_10647"
-[276] "cell_10436" "cell_11592" "cell_9817" "cell_11268" "cell_9961"
-[281] "cell_10071" "cell_9959" "cell_11419" "cell_10585" "cell_11214"
-[286] "cell_11084" "cell_11165" "cell_11327" "cell_11392" "cell_10718"
-[291] "cell_10466" "cell_12090" "cell_11555" "cell_10995" "cell_10526"
-[296] "cell_10761" "cell_11038" "cell_11232" "cell_10715" "cell_10458"
-[301] "cell_10019" "cell_10328" "cell_10411" "cell_10313" "cell_9930"
-[306] "cell_11114" "cell_9936" "cell_11234" "cell_10556" "cell_9846"
-[311] "cell_11871" "cell_11285" "cell_10991" "cell_11939" "cell_10213"
-[316] "cell_9863" "cell_11710" "cell_11256" "cell_10147" "cell_9989"
-[321] "cell_10464" "cell_10953" "cell_10388" "cell_10216" "cell_10010"
-[326] "cell_11485" "cell_10695" "cell_11760" "cell_11328" "cell_11620"
-[331] "cell_10694" "cell_10175" "cell_9997" "cell_12147" "cell_10553"
-[336] "cell_11266" "cell_10467" "cell_11233" "cell_10963" "cell_12149"
-[341] "cell_9986" "cell_11276" "cell_11904" "cell_12179" "cell_9847"
-[346] "cell_11303" "cell_11299" "cell_10956" "cell_10347" "cell_11599"
-[351] "cell_10697" "cell_10190" "cell_10261" "cell_10498" "cell_11588"
-[356] "cell_9977" "cell_11839" "cell_11777" "cell_11941" "cell_10645"
-[361] "cell_10126" "cell_10833" "cell_10672" "cell_10654" "cell_11024"
-[366] "cell_10164" "cell_11522" "cell_10407" "cell_12134" "cell_11056"
-[371] "cell_11489" "cell_9969" "cell_9820" "cell_11017" "cell_9835"
-[376] "cell_12064" "cell_11562" "cell_10345" "cell_10225" "cell_10783"
-[381] "cell_12036" "cell_11333" "cell_10812" "cell_10998" "cell_9892"
-[386] "cell_10360" "cell_12152" "cell_10508" "cell_9813" "cell_11124"
-[391] "cell_11073" "cell_9859" "cell_10421" "cell_10930" "cell_10374"
-[396] "cell_12097" "cell_11217" "cell_10800" "cell_11063" "cell_10363"
-[401] "cell_10515" "cell_10267" "cell_11047" "cell_11744" "cell_11564"
-[406] "cell_9849" "cell_11916" "cell_12082" "cell_12057" "cell_10664"
-[411] "cell_11680" "cell_11542" "cell_10765" "cell_12066" "cell_11438"
-[416] "cell_12072" "cell_10441" "cell_10396" "cell_10838" "cell_9832"
-[421] "cell_10299" "cell_11769" "cell_11402" "cell_11736" "cell_11012"
-[426] "cell_11484" "cell_11962" "cell_10604" "cell_11966" "cell_10370"
-[431] "cell_10099" "cell_10669" "cell_11774" "cell_11579" "cell_10059"
-[436] "cell_10511" "cell_10597" "cell_12031" "cell_10961" "cell_10497"
-[441] "cell_11934" "cell_11353" "cell_11133" "cell_9837" "cell_11112"
-[446] "cell_10272" "cell_10868" "cell_11734" "cell_10554" "cell_11683"
-[451] "cell_10898" "cell_10623" "cell_10864" "cell_10217" "cell_10739"
-[456] "cell_12174" "cell_12053" "cell_11859" "cell_10103" "cell_12167"
-[461] "cell_10848" "cell_9975" "cell_10204" "cell_11678" "cell_10769"
-[466] "cell_10369" "cell_10155" "cell_10860" "cell_10512" "cell_10333"
-[471] "cell_11149" "cell_10560" "cell_10510" "cell_11658" "cell_10354"
-[476] "cell_11141" "cell_11263" "cell_12058" "cell_9856" "cell_11208"
-[481] "cell_9779" "cell_11598" "cell_10231" "cell_11547" "cell_10468"
-[486] "cell_11961" "cell_10610" "cell_10453" "cell_10048" "cell_11304"
-[491] "cell_10571" "cell_11778" "cell_10546" "cell_12111" "cell_11120"
-[496] "cell_9940" "cell_12040" "cell_11471" "cell_11470" "cell_11321"
-[501] "cell_10236" "cell_11176" "cell_12094" "cell_10509" "cell_10133"
-[506] "cell_10359" "cell_11595" "cell_11019" "cell_10602" "cell_11414"
-[511] "cell_11838" "cell_11932" "cell_11057" "cell_10303" "cell_10750"
-[516] "cell_9880" "cell_10224" "cell_10885" "cell_11281" "cell_10399"
-[521] "cell_9816" "cell_10737" "cell_10250" "cell_11040" "cell_9873"
-[526] "cell_11782" "cell_10227" "cell_12125" "cell_11714" "cell_11104"
-[531] "cell_11354" "cell_10660" "cell_9907" "cell_10249" "cell_10611"
-[536] "cell_10018" "cell_11389" "cell_10098" "cell_10401" "cell_11418"
-[541] "cell_12092" "cell_10890" "cell_10850" "cell_11791" "cell_11988"
-[546] "cell_11897" "cell_10026" "cell_10403" "cell_10030" "cell_11688"
-[551] "cell_11571" "cell_10696" "cell_9974" "cell_9967" "cell_11381"
-[556] "cell_11972" "cell_12143" "cell_11837" "cell_10521" "cell_11280"
-[561] "cell_11694" "cell_10166" "cell_11010" "cell_10947" "cell_11901"
-[566] "cell_12044" "cell_10586" "cell_10428" "cell_10115" "cell_11357"
-[571] "cell_11121" "cell_12114" "cell_12076" "cell_9823" "cell_11162"
-[576] "cell_10836" "cell_11954" "cell_11713" "cell_11168" "cell_10700"
-[581] "cell_11845" "cell_11557" "cell_11346" "cell_9962" "cell_11386"
-[586] "cell_11799" "cell_10869" "cell_11411" "cell_10766" "cell_11450"
-[591] "cell_11058" "cell_10481" "cell_10123" "cell_10238" "cell_10107"
-[596] "cell_9968" "cell_11951" "cell_11811" "cell_11519" "cell_11172"
-[601] "cell_10661" "cell_10534" "cell_10904" "cell_12081" "cell_10237"
-[606] "cell_10247" "cell_10380" "cell_11199" "cell_11447" "cell_11854"
-[611] "cell_11524" "cell_10058" "cell_11586" "cell_10234" "cell_11743"
-[616] "cell_10256" "cell_11775" "cell_11270" "cell_10089" "cell_9777"
-[621] "cell_10635" "cell_10049" "cell_10410" "cell_10675" "cell_10476"
-[626] "cell_10832" "cell_10940" "cell_10788" "cell_11818" "cell_11502"
-[631] "cell_10731" "cell_12166" "cell_10646" "cell_11397" "cell_10151"
-[636] "cell_12085" "cell_11435" "cell_10239" "cell_11715" "cell_12060"
-[641] "cell_11798" "cell_9929" "cell_10189" "cell_10212" "cell_9797"
-[646] "cell_11529" "cell_11033" "cell_11794" "cell_9812" "cell_9992"
-[651] "cell_11696" "cell_10680" "cell_10319" "cell_10120" "cell_10601"
-[656] "cell_12145" "cell_10451" "cell_11243" "cell_9824" "cell_11070"
-[661] "cell_11983" "cell_11986" "cell_10422" "cell_11664" "cell_10143"
-[666] "cell_11368" "cell_11580" "cell_11583" "cell_11312" "cell_11862"
-[671] "cell_11493" "cell_11226" "cell_9785" "cell_10417" "cell_9931"
-[676] "cell_11277" "cell_11261" "cell_11642" "cell_10977" "cell_10424"
-[681] "cell_10588" "cell_9803" "cell_11938" "cell_11877" "cell_10271"
-[686] "cell_10177" "cell_10437" "cell_10741" "cell_10580" "cell_11102"
-[691] "cell_10945" "cell_11077" "cell_9916" "cell_9861" "cell_10037"
-[696] "cell_10485" "cell_10443" "cell_10140" "cell_10285" "cell_11618"
-[701] "cell_9845" "cell_11469" "cell_11140" "cell_10452" "cell_10352"
-[706] "cell_9894" "cell_11823" "cell_10944" "cell_10488" "cell_10867"
-[711] "cell_11516" "cell_12116" "cell_10755" "cell_10072" "cell_11393"
-[716] "cell_11650" "cell_10878" "cell_11400" "cell_9868" "cell_10817"
-[721] "cell_11700" "cell_11085" "cell_12007" "cell_11998" "cell_12158"
-[726] "cell_10315" "cell_10698" "cell_10471" "cell_10111" "cell_11945"
-[731] "cell_10999" "cell_11225" "cell_11083" "cell_11539" "cell_12113"
-[736] "cell_11158" "cell_9802" "cell_11173" "cell_10034" "cell_10193"
-[741] "cell_12083" "cell_11296" "cell_11007" "cell_10895" "cell_10725"
-[746] "cell_11709" "cell_10626" "cell_10168" "cell_9770" "cell_10870"
-[751] "cell_10950" "cell_9924" "cell_12006" "cell_9983" "cell_10787"
-[756] "cell_10054" "cell_11118" "cell_10732" "cell_10198" "cell_11923"
-[761] "cell_10518" "cell_10418" "cell_10484" "cell_10522" "cell_10153"
-[766] "cell_11483" "cell_11309" "cell_11445" "cell_11754" "cell_11914"
-[771] "cell_10677" "cell_11772" "cell_11697" "cell_9942" "cell_10202"
-[776] "cell_10383" "cell_11074" "cell_11212" "cell_10572" "cell_11342"
-[781] "cell_10593" "cell_10283" "cell_12056" "cell_9819" "cell_11771"
-[786] "cell_11591" "cell_9998" "cell_11144" "cell_11015" "cell_10381"
-[791] "cell_10937" "cell_11265" "cell_10086" "cell_10187" "cell_10215"
-[796] "cell_11611" "cell_9911" "cell_11308" "cell_10735" "cell_11978"
-[801] "cell_11067" "cell_10491" "cell_11003" "cell_10989" "cell_11480"
-[806] "cell_10255" "cell_10312" "cell_11548" "cell_11207" "cell_9920"
-[811] "cell_10209" "cell_11211" "cell_11422" "cell_11360" "cell_10305"
-[816] "cell_10821" "cell_10461" "cell_10008" "cell_10801" "cell_11319"
-[821] "cell_10078" "cell_11651" "cell_11287" "cell_10389" "cell_10135"
-[826] "cell_10773" "cell_11246" "cell_11623" "cell_11627" "cell_11031"
-[831] "cell_10200" "cell_11113" "cell_9794" "cell_12023" "cell_11197"
-[836] "cell_11313" "cell_11129" "cell_11597" "cell_9807" "cell_10095"
-[841] "cell_11860"
-
-
-$Mesenchyme
-$Mesenchyme$aucThr
-$Mesenchyme$aucThr$selected
-minimumDens
- 0.418
-
-$Mesenchyme$aucThr$thresholds
- threshold nCells
-Global_k1 0.261 168
-L_k2 0.374 95
-R_k3 0.171 346
-minimumDens 0.418 81
-
-$Mesenchyme$aucThr$comment
-[1] ""
-
-
-$Mesenchyme$assignment
- [1] "cell_10062" "cell_11100" "cell_12059" "cell_10387" "cell_9919"
- [6] "cell_10754" "cell_12075" "cell_10474" "cell_10480" "cell_11081"
-[11] "cell_10125" "cell_12162" "cell_11465" "cell_11840" "cell_9784"
-[16] "cell_11204" "cell_10900" "cell_9938" "cell_10394" "cell_11377"
-[21] "cell_11407" "cell_10367" "cell_9961" "cell_9930" "cell_11710"
-[26] "cell_10388" "cell_12147" "cell_10963" "cell_11276" "cell_10498"
-[31] "cell_10645" "cell_10164" "cell_11489" "cell_9969" "cell_12064"
-[36] "cell_10363" "cell_12072" "cell_10669" "cell_10511" "cell_11934"
-[41] "cell_10864" "cell_10204" "cell_10155" "cell_11208" "cell_11120"
-[46] "cell_9880" "cell_10250" "cell_12092" "cell_11897" "cell_11571"
-[51] "cell_11837" "cell_11010" "cell_10947" "cell_12044" "cell_11954"
-[56] "cell_9962" "cell_10237" "cell_11502" "cell_10151" "cell_11435"
-[61] "cell_12060" "cell_10451" "cell_11243" "cell_11070" "cell_11983"
-[66] "cell_11580" "cell_11583" "cell_9785" "cell_10177" "cell_10485"
-[71] "cell_11469" "cell_12113" "cell_10677" "cell_10383" "cell_11015"
-[76] "cell_10491" "cell_11480" "cell_10461" "cell_10389" "cell_9794"
-[81] "cell_9807"
-
-
-$`Neural crest`
-$`Neural crest`$aucThr
-$`Neural crest`$aucThr$selected
-outlierOfGlobal
- 0.331
-
-$`Neural crest`$aucThr$thresholds
- threshold nCells
-outlierOfGlobal 0.331 0
-Global_k1 0.181 264
-L_k2 0.168 373
-R_k3 0.254 12
-
-$`Neural crest`$aucThr$comment
-[1] "The AUC might follow a normal distribution (random gene-set?). The right distribution is taller. "
-
-
-$`Neural crest`$assignment
-character(0)
-
-
-$NMP
-$NMP$aucThr
-$NMP$aucThr$selected
- L_k2
-0.314
-
-$NMP$aucThr$thresholds
- threshold nCells
-Global_k1 0.1873 195
-L_k2 0.3143 42
-R_k3 0.0961 677
-
-$NMP$aucThr$comment
-[1] ""
-
-
-$NMP$assignment
- [1] "cell_11021" "cell_10721" "cell_10116" "cell_10248" "cell_12052"
- [6] "cell_10440" "cell_11380" "cell_9851" "cell_10886" "cell_11239"
-[11] "cell_11180" "cell_10647" "cell_10411" "cell_11234" "cell_12149"
-[16] "cell_9977" "cell_9820" "cell_12097" "cell_10597" "cell_10868"
-[21] "cell_11149" "cell_10231" "cell_10453" "cell_11040" "cell_11104"
-[26] "cell_10696" "cell_10380" "cell_10234" "cell_10832" "cell_9929"
-[31] "cell_9824" "cell_11368" "cell_10140" "cell_11393" "cell_11998"
-[36] "cell_10698" "cell_11083" "cell_12006" "cell_11207" "cell_10821"
-[41] "cell_11319" "cell_11597"
-
-
-$`Paraxial mesoderm`
-$`Paraxial mesoderm`$aucThr
-$`Paraxial mesoderm`$aucThr$selected
-minimumDens
- 0.0736
-
-$`Paraxial mesoderm`$aucThr$thresholds
- threshold nCells
-Global_k1 0.1970 181
-L_k2 0.5372 0
-R_k3 0.0667 841
-minimumDens 0.0736 840
-
-$`Paraxial mesoderm`$aucThr$comment
-[1] "The global distribution overlaps the partial distributions. "
-
-
-$`Paraxial mesoderm`$assignment
- [1] "cell_11995" "cell_9963" "cell_10910" "cell_11021" "cell_10433"
- [6] "cell_11395" "cell_10779" "cell_10883" "cell_10721" "cell_10116"
- [11] "cell_10785" "cell_11781" "cell_11147" "cell_11842" "cell_11218"
- [16] "cell_11441" "cell_11558" "cell_9979" "cell_10323" "cell_11663"
- [21] "cell_10935" "cell_11567" "cell_10673" "cell_11634" "cell_10815"
- [26] "cell_10077" "cell_9934" "cell_11888" "cell_10356" "cell_10490"
- [31] "cell_9921" "cell_10062" "cell_9809" "cell_11906" "cell_10951"
- [36] "cell_10520" "cell_12176" "cell_11850" "cell_10284" "cell_9781"
- [41] "cell_11885" "cell_11687" "cell_10523" "cell_11100" "cell_10881"
- [46] "cell_10774" "cell_12107" "cell_11216" "cell_10439" "cell_10902"
- [51] "cell_10856" "cell_11702" "cell_11269" "cell_10248" "cell_11883"
- [56] "cell_11682" "cell_10877" "cell_9933" "cell_10843" "cell_11154"
- [61] "cell_12052" "cell_9895" "cell_12028" "cell_10454" "cell_11750"
- [66] "cell_12059" "cell_10615" "cell_10751" "cell_10387" "cell_10245"
- [71] "cell_11767" "cell_9919" "cell_11976" "cell_11971" "cell_10797"
- [76] "cell_10094" "cell_11724" "cell_11030" "cell_11855" "cell_10754"
- [81] "cell_9905" "cell_11530" "cell_11352" "cell_10357" "cell_12074"
- [86] "cell_12012" "cell_11561" "cell_11398" "cell_12075" "cell_12177"
- [91] "cell_11653" "cell_10644" "cell_11993" "cell_10322" "cell_11900"
- [96] "cell_11315" "cell_10474" "cell_10480" "cell_11220" "cell_10440"
-[101] "cell_11596" "cell_10296" "cell_11337" "cell_11856" "cell_11728"
-[106] "cell_10241" "cell_12016" "cell_11770" "cell_10917" "cell_11805"
-[111] "cell_12002" "cell_10599" "cell_10846" "cell_10687" "cell_11330"
-[116] "cell_11081" "cell_9953" "cell_10181" "cell_10395" "cell_12021"
-[121] "cell_11667" "cell_10547" "cell_11329" "cell_10332" "cell_10562"
-[126] "cell_11183" "cell_11138" "cell_10385" "cell_10125" "cell_10047"
-[131] "cell_10038" "cell_10386" "cell_11673" "cell_10105" "cell_12162"
-[136] "cell_10749" "cell_11549" "cell_11458" "cell_11290" "cell_11213"
-[141] "cell_10849" "cell_11465" "cell_9885" "cell_10416" "cell_10847"
-[146] "cell_11009" "cell_11733" "cell_10756" "cell_10479" "cell_11260"
-[151] "cell_11002" "cell_10117" "cell_10933" "cell_11840" "cell_10922"
-[156] "cell_11495" "cell_11380" "cell_10478" "cell_11026" "cell_11880"
-[161] "cell_11896" "cell_12110" "cell_11115" "cell_10559" "cell_12151"
-[166] "cell_11109" "cell_11014" "cell_11526" "cell_11018" "cell_11582"
-[171] "cell_11476" "cell_10065" "cell_10628" "cell_11603" "cell_10825"
-[176] "cell_9851" "cell_10634" "cell_10791" "cell_9844" "cell_10886"
-[181] "cell_11931" "cell_11975" "cell_11150" "cell_10450" "cell_12115"
-[186] "cell_11506" "cell_11239" "cell_11130" "cell_10011" "cell_11922"
-[191] "cell_11827" "cell_10393" "cell_11982" "cell_10229" "cell_12140"
-[196] "cell_9799" "cell_10907" "cell_11957" "cell_9784" "cell_11204"
-[201] "cell_10292" "cell_11229" "cell_10692" "cell_11370" "cell_9972"
-[206] "cell_10914" "cell_10027" "cell_10262" "cell_11657" "cell_11552"
-[211] "cell_12029" "cell_11123" "cell_10900" "cell_11093" "cell_9778"
-[216] "cell_9938" "cell_11001" "cell_11619" "cell_12160" "cell_9876"
-[221] "cell_9776" "cell_10394" "cell_10029" "cell_11377" "cell_11679"
-[226] "cell_11054" "cell_11528" "cell_11913" "cell_11515" "cell_10435"
-[231] "cell_10758" "cell_10220" "cell_10624" "cell_11716" "cell_11371"
-[236] "cell_12042" "cell_10414" "cell_10828" "cell_10659" "cell_11424"
-[241] "cell_11096" "cell_12171" "cell_11803" "cell_11404" "cell_11180"
-[246] "cell_10046" "cell_10009" "cell_9792" "cell_11853" "cell_11095"
-[251] "cell_11511" "cell_11835" "cell_11463" "cell_10146" "cell_10317"
-[256] "cell_11407" "cell_12173" "cell_10161" "cell_10438" "cell_10981"
-[261] "cell_10079" "cell_11210" "cell_11174" "cell_10876" "cell_10087"
-[266] "cell_11630" "cell_11434" "cell_9888" "cell_10367" "cell_11107"
-[271] "cell_11994" "cell_10192" "cell_11822" "cell_10647" "cell_10436"
-[276] "cell_11592" "cell_9817" "cell_11268" "cell_9961" "cell_10071"
-[281] "cell_9959" "cell_11419" "cell_10585" "cell_11214" "cell_11084"
-[286] "cell_11165" "cell_11327" "cell_11392" "cell_10718" "cell_10466"
-[291] "cell_12090" "cell_11555" "cell_10995" "cell_10526" "cell_10761"
-[296] "cell_11038" "cell_11232" "cell_10715" "cell_10458" "cell_10019"
-[301] "cell_10328" "cell_10411" "cell_10313" "cell_9930" "cell_11114"
-[306] "cell_9936" "cell_11234" "cell_10556" "cell_9846" "cell_11871"
-[311] "cell_11285" "cell_10991" "cell_11939" "cell_10213" "cell_9863"
-[316] "cell_11710" "cell_11256" "cell_10147" "cell_9989" "cell_10464"
-[321] "cell_10953" "cell_10388" "cell_10216" "cell_10010" "cell_11485"
-[326] "cell_10695" "cell_11760" "cell_11328" "cell_11620" "cell_10694"
-[331] "cell_10175" "cell_9997" "cell_12147" "cell_10553" "cell_11266"
-[336] "cell_10467" "cell_11233" "cell_10963" "cell_12149" "cell_9986"
-[341] "cell_11276" "cell_11904" "cell_12179" "cell_9847" "cell_11303"
-[346] "cell_11299" "cell_10956" "cell_10347" "cell_11599" "cell_10697"
-[351] "cell_10190" "cell_10261" "cell_10498" "cell_11588" "cell_9977"
-[356] "cell_11839" "cell_11777" "cell_11941" "cell_10645" "cell_10126"
-[361] "cell_10833" "cell_10672" "cell_10654" "cell_11024" "cell_10164"
-[366] "cell_11522" "cell_10407" "cell_12134" "cell_11056" "cell_11489"
-[371] "cell_9969" "cell_9820" "cell_11017" "cell_9835" "cell_12064"
-[376] "cell_11562" "cell_10345" "cell_10225" "cell_10783" "cell_12036"
-[381] "cell_11333" "cell_10812" "cell_10998" "cell_9892" "cell_10360"
-[386] "cell_12152" "cell_10508" "cell_9813" "cell_11124" "cell_11073"
-[391] "cell_9859" "cell_10421" "cell_10930" "cell_10374" "cell_12097"
-[396] "cell_11217" "cell_10800" "cell_11063" "cell_10363" "cell_10515"
-[401] "cell_10267" "cell_11047" "cell_11744" "cell_11564" "cell_9849"
-[406] "cell_11916" "cell_12082" "cell_12057" "cell_10664" "cell_11680"
-[411] "cell_11542" "cell_10765" "cell_12066" "cell_11438" "cell_12072"
-[416] "cell_10441" "cell_10396" "cell_10838" "cell_9832" "cell_10299"
-[421] "cell_11769" "cell_11402" "cell_11736" "cell_11012" "cell_11484"
-[426] "cell_11962" "cell_10604" "cell_11966" "cell_10370" "cell_10099"
-[431] "cell_10669" "cell_11774" "cell_11579" "cell_10059" "cell_10511"
-[436] "cell_10597" "cell_12031" "cell_10961" "cell_10497" "cell_11934"
-[441] "cell_11353" "cell_11133" "cell_9837" "cell_11112" "cell_10272"
-[446] "cell_10868" "cell_11734" "cell_10554" "cell_11683" "cell_10898"
-[451] "cell_10623" "cell_10864" "cell_10217" "cell_10739" "cell_12174"
-[456] "cell_12053" "cell_11859" "cell_10103" "cell_12167" "cell_10848"
-[461] "cell_9975" "cell_10204" "cell_11678" "cell_10769" "cell_10369"
-[466] "cell_10155" "cell_10860" "cell_10512" "cell_10333" "cell_11149"
-[471] "cell_10560" "cell_10510" "cell_11658" "cell_10354" "cell_11141"
-[476] "cell_11263" "cell_12058" "cell_9856" "cell_11208" "cell_9779"
-[481] "cell_11598" "cell_10231" "cell_11547" "cell_10468" "cell_11961"
-[486] "cell_10610" "cell_10453" "cell_10048" "cell_11304" "cell_10571"
-[491] "cell_11778" "cell_10546" "cell_12111" "cell_11120" "cell_9940"
-[496] "cell_12040" "cell_11471" "cell_11470" "cell_11321" "cell_10236"
-[501] "cell_11176" "cell_12094" "cell_10509" "cell_10133" "cell_10359"
-[506] "cell_11595" "cell_11019" "cell_10602" "cell_11414" "cell_11838"
-[511] "cell_11932" "cell_11057" "cell_10303" "cell_10750" "cell_9880"
-[516] "cell_10224" "cell_10885" "cell_11281" "cell_10399" "cell_9816"
-[521] "cell_10737" "cell_10250" "cell_11040" "cell_9873" "cell_11782"
-[526] "cell_10227" "cell_12125" "cell_11714" "cell_11104" "cell_11354"
-[531] "cell_10660" "cell_9907" "cell_10249" "cell_10611" "cell_10018"
-[536] "cell_11389" "cell_10098" "cell_10401" "cell_11418" "cell_12092"
-[541] "cell_10890" "cell_10850" "cell_11791" "cell_11988" "cell_11897"
-[546] "cell_10026" "cell_10403" "cell_10030" "cell_11688" "cell_11571"
-[551] "cell_10696" "cell_9974" "cell_9967" "cell_11381" "cell_11972"
-[556] "cell_12143" "cell_11837" "cell_10521" "cell_11280" "cell_11694"
-[561] "cell_10166" "cell_11010" "cell_10947" "cell_11901" "cell_12044"
-[566] "cell_10586" "cell_10428" "cell_10115" "cell_11357" "cell_11121"
-[571] "cell_12114" "cell_12076" "cell_9823" "cell_11162" "cell_10836"
-[576] "cell_11954" "cell_11713" "cell_11168" "cell_10700" "cell_11845"
-[581] "cell_11557" "cell_11346" "cell_9962" "cell_11386" "cell_11799"
-[586] "cell_10869" "cell_11411" "cell_10766" "cell_11450" "cell_11058"
-[591] "cell_10481" "cell_10123" "cell_10238" "cell_10107" "cell_9968"
-[596] "cell_11951" "cell_11811" "cell_11519" "cell_11172" "cell_10661"
-[601] "cell_10534" "cell_10904" "cell_12081" "cell_10237" "cell_10247"
-[606] "cell_10380" "cell_11199" "cell_11447" "cell_11854" "cell_11524"
-[611] "cell_10058" "cell_11586" "cell_10234" "cell_11743" "cell_10256"
-[616] "cell_11775" "cell_11270" "cell_10089" "cell_9777" "cell_10635"
-[621] "cell_10049" "cell_10410" "cell_10675" "cell_10476" "cell_10832"
-[626] "cell_10940" "cell_10788" "cell_11818" "cell_11502" "cell_10731"
-[631] "cell_12166" "cell_10646" "cell_11397" "cell_10151" "cell_12085"
-[636] "cell_11435" "cell_10239" "cell_11715" "cell_12060" "cell_11798"
-[641] "cell_9929" "cell_10189" "cell_10212" "cell_9797" "cell_11529"
-[646] "cell_11033" "cell_11794" "cell_9812" "cell_9992" "cell_11696"
-[651] "cell_10680" "cell_10319" "cell_10120" "cell_10601" "cell_12145"
-[656] "cell_10451" "cell_11243" "cell_9824" "cell_11070" "cell_11983"
-[661] "cell_11986" "cell_10422" "cell_11664" "cell_10143" "cell_11368"
-[666] "cell_11580" "cell_11583" "cell_11312" "cell_11862" "cell_11493"
-[671] "cell_11226" "cell_9785" "cell_10417" "cell_9931" "cell_11277"
-[676] "cell_11261" "cell_11642" "cell_10977" "cell_10424" "cell_10588"
-[681] "cell_9803" "cell_11938" "cell_11877" "cell_10271" "cell_10177"
-[686] "cell_10437" "cell_10741" "cell_10580" "cell_11102" "cell_10945"
-[691] "cell_11077" "cell_9916" "cell_9861" "cell_10037" "cell_10485"
-[696] "cell_10443" "cell_10140" "cell_10285" "cell_11618" "cell_9845"
-[701] "cell_11469" "cell_11140" "cell_10452" "cell_10352" "cell_9894"
-[706] "cell_11823" "cell_10944" "cell_10488" "cell_10867" "cell_11516"
-[711] "cell_12116" "cell_10755" "cell_10072" "cell_11393" "cell_11650"
-[716] "cell_10878" "cell_11400" "cell_9868" "cell_10817" "cell_11700"
-[721] "cell_11085" "cell_12007" "cell_11998" "cell_12158" "cell_10315"
-[726] "cell_10698" "cell_10471" "cell_10111" "cell_11945" "cell_10999"
-[731] "cell_11225" "cell_11083" "cell_11539" "cell_12113" "cell_11158"
-[736] "cell_9802" "cell_11173" "cell_10034" "cell_10193" "cell_12083"
-[741] "cell_11296" "cell_11007" "cell_10895" "cell_10725" "cell_11709"
-[746] "cell_10626" "cell_10168" "cell_9770" "cell_10870" "cell_10950"
-[751] "cell_9924" "cell_12006" "cell_9983" "cell_10787" "cell_10054"
-[756] "cell_11118" "cell_10732" "cell_10198" "cell_11923" "cell_10518"
-[761] "cell_10418" "cell_10484" "cell_10522" "cell_10153" "cell_11483"
-[766] "cell_11309" "cell_11445" "cell_11754" "cell_11914" "cell_10677"
-[771] "cell_11772" "cell_11697" "cell_9942" "cell_10202" "cell_10383"
-[776] "cell_11074" "cell_11212" "cell_10572" "cell_11342" "cell_10593"
-[781] "cell_10283" "cell_12056" "cell_9819" "cell_11771" "cell_11591"
-[786] "cell_9998" "cell_11144" "cell_11015" "cell_10381" "cell_10937"
-[791] "cell_11265" "cell_10086" "cell_10187" "cell_10215" "cell_11611"
-[796] "cell_9911" "cell_11308" "cell_10735" "cell_11978" "cell_11067"
-[801] "cell_10491" "cell_11003" "cell_10989" "cell_11480" "cell_10255"
-[806] "cell_10312" "cell_11548" "cell_11207" "cell_9920" "cell_10209"
-[811] "cell_11211" "cell_11422" "cell_11360" "cell_10305" "cell_10821"
-[816] "cell_10461" "cell_10008" "cell_10801" "cell_11319" "cell_10078"
-[821] "cell_11651" "cell_11287" "cell_10389" "cell_10135" "cell_10773"
-[826] "cell_11246" "cell_11623" "cell_11627" "cell_11031" "cell_10200"
-[831] "cell_11113" "cell_9794" "cell_12023" "cell_11197" "cell_11313"
-[836] "cell_11129" "cell_11597" "cell_9807" "cell_10095" "cell_11860"
-
-
-$`Pharyngeal mesoderm`
-$`Pharyngeal mesoderm`$aucThr
-$`Pharyngeal mesoderm`$aucThr$selected
-minimumDens
- 0.0816
-
-$`Pharyngeal mesoderm`$aucThr$thresholds
- threshold nCells
-Global_k1 0.2244 228
-L_k2 0.5680 0
-R_k3 0.0893 837
-minimumDens 0.0816 838
-
-$`Pharyngeal mesoderm`$aucThr$comment
-[1] "The global distribution overlaps the partial distributions. "
-
-
-$`Pharyngeal mesoderm`$assignment
- [1] "cell_11995" "cell_9963" "cell_10910" "cell_11021" "cell_10433"
- [6] "cell_11395" "cell_10779" "cell_10883" "cell_10721" "cell_10116"
- [11] "cell_10785" "cell_11781" "cell_11147" "cell_11842" "cell_11218"
- [16] "cell_11441" "cell_11558" "cell_9979" "cell_10323" "cell_11663"
- [21] "cell_10935" "cell_11567" "cell_10673" "cell_11634" "cell_10815"
- [26] "cell_10077" "cell_9934" "cell_11888" "cell_10356" "cell_10490"
- [31] "cell_9921" "cell_10062" "cell_9809" "cell_11906" "cell_10951"
- [36] "cell_10520" "cell_12176" "cell_11850" "cell_10284" "cell_9781"
- [41] "cell_11885" "cell_11687" "cell_10523" "cell_11100" "cell_10881"
- [46] "cell_10774" "cell_12107" "cell_11216" "cell_10439" "cell_10902"
- [51] "cell_10856" "cell_11702" "cell_11269" "cell_10248" "cell_11883"
- [56] "cell_11682" "cell_10877" "cell_9933" "cell_10843" "cell_11154"
- [61] "cell_12052" "cell_9895" "cell_12028" "cell_10454" "cell_11750"
- [66] "cell_12059" "cell_10615" "cell_10751" "cell_10387" "cell_10245"
- [71] "cell_11767" "cell_9919" "cell_11976" "cell_11971" "cell_10797"
- [76] "cell_10094" "cell_11724" "cell_11030" "cell_11855" "cell_10754"
- [81] "cell_9905" "cell_11530" "cell_11352" "cell_10357" "cell_12074"
- [86] "cell_12012" "cell_11561" "cell_11398" "cell_12075" "cell_12177"
- [91] "cell_11653" "cell_10644" "cell_11993" "cell_10322" "cell_11900"
- [96] "cell_11315" "cell_10474" "cell_10480" "cell_11220" "cell_10440"
-[101] "cell_11596" "cell_10296" "cell_11337" "cell_11856" "cell_11728"
-[106] "cell_10241" "cell_12016" "cell_11770" "cell_10917" "cell_11805"
-[111] "cell_12002" "cell_10599" "cell_10846" "cell_10687" "cell_11330"
-[116] "cell_11081" "cell_9953" "cell_10181" "cell_10395" "cell_12021"
-[121] "cell_11667" "cell_10547" "cell_11329" "cell_10332" "cell_10562"
-[126] "cell_11183" "cell_11138" "cell_10385" "cell_10125" "cell_10047"
-[131] "cell_10038" "cell_10386" "cell_11673" "cell_10105" "cell_12162"
-[136] "cell_10749" "cell_11549" "cell_11458" "cell_11290" "cell_11213"
-[141] "cell_10849" "cell_11465" "cell_9885" "cell_10416" "cell_10847"
-[146] "cell_11009" "cell_11733" "cell_10756" "cell_10479" "cell_11260"
-[151] "cell_11002" "cell_10117" "cell_10933" "cell_11840" "cell_10922"
-[156] "cell_11495" "cell_11380" "cell_10478" "cell_11026" "cell_11880"
-[161] "cell_11896" "cell_12110" "cell_11115" "cell_10559" "cell_12151"
-[166] "cell_11109" "cell_11014" "cell_11526" "cell_11018" "cell_11582"
-[171] "cell_11476" "cell_10065" "cell_10628" "cell_11603" "cell_10825"
-[176] "cell_9851" "cell_10634" "cell_10791" "cell_9844" "cell_10886"
-[181] "cell_11931" "cell_11975" "cell_11150" "cell_10450" "cell_12115"
-[186] "cell_11506" "cell_11239" "cell_11130" "cell_10011" "cell_11922"
-[191] "cell_11827" "cell_10393" "cell_11982" "cell_10229" "cell_12140"
-[196] "cell_9799" "cell_10907" "cell_11957" "cell_9784" "cell_11204"
-[201] "cell_10292" "cell_11229" "cell_10692" "cell_11370" "cell_9972"
-[206] "cell_10914" "cell_10027" "cell_10262" "cell_11657" "cell_11552"
-[211] "cell_11123" "cell_10900" "cell_11093" "cell_9778" "cell_9938"
-[216] "cell_11001" "cell_11619" "cell_12160" "cell_9876" "cell_9776"
-[221] "cell_10394" "cell_10029" "cell_11377" "cell_11679" "cell_11054"
-[226] "cell_11528" "cell_11913" "cell_11515" "cell_10435" "cell_10758"
-[231] "cell_10220" "cell_10624" "cell_11716" "cell_11371" "cell_12042"
-[236] "cell_10414" "cell_10828" "cell_10659" "cell_11424" "cell_11096"
-[241] "cell_12171" "cell_11803" "cell_11404" "cell_11180" "cell_10046"
-[246] "cell_10009" "cell_9792" "cell_11853" "cell_11095" "cell_11511"
-[251] "cell_11835" "cell_11463" "cell_10146" "cell_10317" "cell_11407"
-[256] "cell_12173" "cell_10161" "cell_10438" "cell_10981" "cell_10079"
-[261] "cell_11210" "cell_11174" "cell_10876" "cell_10087" "cell_11630"
-[266] "cell_11434" "cell_9888" "cell_10367" "cell_11107" "cell_11994"
-[271] "cell_10192" "cell_11822" "cell_10647" "cell_10436" "cell_11592"
-[276] "cell_9817" "cell_11268" "cell_9961" "cell_10071" "cell_9959"
-[281] "cell_11419" "cell_10585" "cell_11214" "cell_11084" "cell_11165"
-[286] "cell_11327" "cell_11392" "cell_10718" "cell_10466" "cell_12090"
-[291] "cell_11555" "cell_10995" "cell_10526" "cell_10761" "cell_11038"
-[296] "cell_11232" "cell_10715" "cell_10458" "cell_10019" "cell_10328"
-[301] "cell_10411" "cell_10313" "cell_9930" "cell_11114" "cell_9936"
-[306] "cell_11234" "cell_10556" "cell_9846" "cell_11871" "cell_11285"
-[311] "cell_10991" "cell_11939" "cell_10213" "cell_9863" "cell_11710"
-[316] "cell_11256" "cell_10147" "cell_9989" "cell_10464" "cell_10953"
-[321] "cell_10388" "cell_10216" "cell_10010" "cell_11485" "cell_10695"
-[326] "cell_11760" "cell_11328" "cell_11620" "cell_10694" "cell_10175"
-[331] "cell_9997" "cell_12147" "cell_10553" "cell_11266" "cell_10467"
-[336] "cell_11233" "cell_10963" "cell_12149" "cell_9986" "cell_11276"
-[341] "cell_11904" "cell_12179" "cell_9847" "cell_11303" "cell_11299"
-[346] "cell_10956" "cell_10347" "cell_11599" "cell_10697" "cell_10190"
-[351] "cell_10261" "cell_10498" "cell_11588" "cell_9977" "cell_11839"
-[356] "cell_11777" "cell_11941" "cell_10645" "cell_10126" "cell_10833"
-[361] "cell_10672" "cell_10654" "cell_11024" "cell_10164" "cell_11522"
-[366] "cell_10407" "cell_12134" "cell_11056" "cell_11489" "cell_9969"
-[371] "cell_9820" "cell_11017" "cell_9835" "cell_12064" "cell_11562"
-[376] "cell_10345" "cell_10225" "cell_10783" "cell_12036" "cell_11333"
-[381] "cell_10812" "cell_10998" "cell_9892" "cell_10360" "cell_12152"
-[386] "cell_10508" "cell_9813" "cell_11124" "cell_11073" "cell_9859"
-[391] "cell_10421" "cell_10930" "cell_10374" "cell_12097" "cell_11217"
-[396] "cell_10800" "cell_11063" "cell_10363" "cell_10515" "cell_10267"
-[401] "cell_11047" "cell_11744" "cell_11564" "cell_9849" "cell_11916"
-[406] "cell_12082" "cell_12057" "cell_10664" "cell_11680" "cell_11542"
-[411] "cell_10765" "cell_12066" "cell_11438" "cell_12072" "cell_10441"
-[416] "cell_10396" "cell_10838" "cell_9832" "cell_10299" "cell_11769"
-[421] "cell_11402" "cell_11736" "cell_11012" "cell_11484" "cell_11962"
-[426] "cell_10604" "cell_11966" "cell_10370" "cell_10099" "cell_10669"
-[431] "cell_11774" "cell_11579" "cell_10059" "cell_10511" "cell_10597"
-[436] "cell_12031" "cell_10961" "cell_10497" "cell_11934" "cell_11353"
-[441] "cell_11133" "cell_9837" "cell_11112" "cell_10272" "cell_10868"
-[446] "cell_11734" "cell_10554" "cell_11683" "cell_10898" "cell_10623"
-[451] "cell_10864" "cell_10217" "cell_10739" "cell_12174" "cell_12053"
-[456] "cell_11859" "cell_10103" "cell_12167" "cell_10848" "cell_9975"
-[461] "cell_10204" "cell_11678" "cell_10769" "cell_10369" "cell_10155"
-[466] "cell_10860" "cell_10512" "cell_10333" "cell_11149" "cell_10560"
-[471] "cell_10510" "cell_11658" "cell_10354" "cell_11141" "cell_11263"
-[476] "cell_12058" "cell_9856" "cell_11208" "cell_9779" "cell_11598"
-[481] "cell_10231" "cell_11547" "cell_10468" "cell_11961" "cell_10610"
-[486] "cell_10453" "cell_10048" "cell_11304" "cell_10571" "cell_11778"
-[491] "cell_10546" "cell_12111" "cell_11120" "cell_9940" "cell_12040"
-[496] "cell_11471" "cell_11470" "cell_11321" "cell_10236" "cell_11176"
-[501] "cell_12094" "cell_10509" "cell_10133" "cell_10359" "cell_11595"
-[506] "cell_11019" "cell_10602" "cell_11414" "cell_11838" "cell_11932"
-[511] "cell_11057" "cell_10303" "cell_10750" "cell_9880" "cell_10224"
-[516] "cell_10885" "cell_11281" "cell_10399" "cell_9816" "cell_10737"
-[521] "cell_10250" "cell_11040" "cell_9873" "cell_11782" "cell_10227"
-[526] "cell_12125" "cell_11714" "cell_11104" "cell_11354" "cell_10660"
-[531] "cell_9907" "cell_10249" "cell_10611" "cell_10018" "cell_11389"
-[536] "cell_10098" "cell_10401" "cell_11418" "cell_12092" "cell_10890"
-[541] "cell_10850" "cell_11791" "cell_11988" "cell_11897" "cell_10026"
-[546] "cell_10403" "cell_10030" "cell_11688" "cell_11571" "cell_10696"
-[551] "cell_9974" "cell_9967" "cell_11381" "cell_11972" "cell_12143"
-[556] "cell_11837" "cell_10521" "cell_11280" "cell_11694" "cell_10166"
-[561] "cell_11010" "cell_10947" "cell_11901" "cell_12044" "cell_10586"
-[566] "cell_10428" "cell_10115" "cell_11357" "cell_11121" "cell_12114"
-[571] "cell_12076" "cell_9823" "cell_11162" "cell_10836" "cell_11954"
-[576] "cell_11713" "cell_11168" "cell_10700" "cell_11845" "cell_11557"
-[581] "cell_11346" "cell_9962" "cell_11799" "cell_10869" "cell_11411"
-[586] "cell_10766" "cell_11450" "cell_11058" "cell_10481" "cell_10123"
-[591] "cell_10238" "cell_10107" "cell_9968" "cell_11951" "cell_11811"
-[596] "cell_11519" "cell_11172" "cell_10661" "cell_10534" "cell_10904"
-[601] "cell_12081" "cell_10237" "cell_10247" "cell_10380" "cell_11199"
-[606] "cell_11447" "cell_11854" "cell_11524" "cell_10058" "cell_11586"
-[611] "cell_10234" "cell_11743" "cell_10256" "cell_11775" "cell_11270"
-[616] "cell_10089" "cell_9777" "cell_10635" "cell_10049" "cell_10410"
-[621] "cell_10675" "cell_10476" "cell_10832" "cell_10940" "cell_10788"
-[626] "cell_11818" "cell_11502" "cell_10731" "cell_12166" "cell_10646"
-[631] "cell_11397" "cell_10151" "cell_12085" "cell_11435" "cell_10239"
-[636] "cell_11715" "cell_12060" "cell_11798" "cell_9929" "cell_10189"
-[641] "cell_10212" "cell_9797" "cell_11529" "cell_11033" "cell_11794"
-[646] "cell_9812" "cell_9992" "cell_11696" "cell_10680" "cell_10319"
-[651] "cell_10120" "cell_10601" "cell_12145" "cell_10451" "cell_11243"
-[656] "cell_9824" "cell_11070" "cell_11983" "cell_11986" "cell_10422"
-[661] "cell_11664" "cell_10143" "cell_11368" "cell_11580" "cell_11583"
-[666] "cell_11312" "cell_11862" "cell_11493" "cell_11226" "cell_9785"
-[671] "cell_10417" "cell_9931" "cell_11277" "cell_11261" "cell_11642"
-[676] "cell_10977" "cell_10424" "cell_10588" "cell_9803" "cell_11938"
-[681] "cell_11877" "cell_10271" "cell_10177" "cell_10437" "cell_10741"
-[686] "cell_10580" "cell_11102" "cell_10945" "cell_11077" "cell_9916"
-[691] "cell_9861" "cell_10037" "cell_10485" "cell_10443" "cell_10140"
-[696] "cell_10285" "cell_11618" "cell_9845" "cell_11469" "cell_11140"
-[701] "cell_10452" "cell_10352" "cell_9894" "cell_11823" "cell_10944"
-[706] "cell_10488" "cell_10867" "cell_11516" "cell_12116" "cell_10755"
-[711] "cell_10072" "cell_11393" "cell_11650" "cell_10878" "cell_11400"
-[716] "cell_9868" "cell_10817" "cell_11700" "cell_11085" "cell_12007"
-[721] "cell_11998" "cell_12158" "cell_10315" "cell_10698" "cell_10471"
-[726] "cell_10111" "cell_11945" "cell_10999" "cell_11225" "cell_11083"
-[731] "cell_11539" "cell_12113" "cell_11158" "cell_9802" "cell_11173"
-[736] "cell_10034" "cell_10193" "cell_12083" "cell_11296" "cell_11007"
-[741] "cell_10895" "cell_10725" "cell_11709" "cell_10626" "cell_10168"
-[746] "cell_9770" "cell_10870" "cell_10950" "cell_9924" "cell_12006"
-[751] "cell_9983" "cell_10787" "cell_10054" "cell_11118" "cell_10732"
-[756] "cell_10198" "cell_11923" "cell_10518" "cell_10418" "cell_10484"
-[761] "cell_10522" "cell_10153" "cell_11483" "cell_11309" "cell_11445"
-[766] "cell_11754" "cell_11914" "cell_10677" "cell_11772" "cell_11697"
-[771] "cell_9942" "cell_10202" "cell_10383" "cell_11074" "cell_11212"
-[776] "cell_10572" "cell_11342" "cell_10593" "cell_10283" "cell_12056"
-[781] "cell_9819" "cell_11771" "cell_11591" "cell_9998" "cell_11144"
-[786] "cell_11015" "cell_10381" "cell_10937" "cell_11265" "cell_10086"
-[791] "cell_10187" "cell_10215" "cell_11611" "cell_9911" "cell_11308"
-[796] "cell_10735" "cell_11978" "cell_11067" "cell_10491" "cell_11003"
-[801] "cell_10989" "cell_11480" "cell_10255" "cell_10312" "cell_11548"
-[806] "cell_11207" "cell_9920" "cell_10209" "cell_11211" "cell_11422"
-[811] "cell_11360" "cell_10305" "cell_10821" "cell_10461" "cell_10008"
-[816] "cell_10801" "cell_11319" "cell_10078" "cell_11651" "cell_11287"
-[821] "cell_10389" "cell_10135" "cell_10773" "cell_11246" "cell_11623"
-[826] "cell_11627" "cell_11031" "cell_10200" "cell_11113" "cell_9794"
-[831] "cell_12023" "cell_11197" "cell_11313" "cell_11129" "cell_11597"
-[836] "cell_9807" "cell_10095" "cell_11860"
-
-
-$`Somitic mesoderm`
-$`Somitic mesoderm`$aucThr
-$`Somitic mesoderm`$aucThr$selected
-minimumDens
- 0.0567
-
-$`Somitic mesoderm`$aucThr$thresholds
- threshold nCells
-Global_k1 0.1638 171
-L_k2 0.1739 159
-minimumDens 0.0567 839
-
-$`Somitic mesoderm`$aucThr$comment
-[1] "The global distribution overlaps the partial distributions. "
-
-
-$`Somitic mesoderm`$assignment
- [1] "cell_11995" "cell_9963" "cell_10910" "cell_11021" "cell_10433"
- [6] "cell_11395" "cell_10779" "cell_10883" "cell_10721" "cell_10116"
- [11] "cell_10785" "cell_11781" "cell_11147" "cell_11842" "cell_11218"
- [16] "cell_11441" "cell_11558" "cell_9979" "cell_10323" "cell_11663"
- [21] "cell_10935" "cell_11567" "cell_10673" "cell_11634" "cell_10815"
- [26] "cell_10077" "cell_9934" "cell_11888" "cell_10356" "cell_10490"
- [31] "cell_9921" "cell_10062" "cell_9809" "cell_11906" "cell_10084"
- [36] "cell_10951" "cell_10520" "cell_10142" "cell_12176" "cell_11850"
- [41] "cell_10284" "cell_9781" "cell_11885" "cell_11687" "cell_10523"
- [46] "cell_11100" "cell_10881" "cell_10774" "cell_12107" "cell_11216"
- [51] "cell_10439" "cell_10902" "cell_10856" "cell_11702" "cell_11269"
- [56] "cell_10248" "cell_11883" "cell_11682" "cell_10877" "cell_9933"
- [61] "cell_10843" "cell_11154" "cell_12052" "cell_9895" "cell_12028"
- [66] "cell_10454" "cell_11750" "cell_12059" "cell_10615" "cell_10751"
- [71] "cell_10387" "cell_10245" "cell_11767" "cell_9919" "cell_11976"
- [76] "cell_11971" "cell_10797" "cell_10094" "cell_11724" "cell_11030"
- [81] "cell_11855" "cell_10754" "cell_9905" "cell_11530" "cell_11352"
- [86] "cell_10357" "cell_12074" "cell_12012" "cell_11561" "cell_11398"
- [91] "cell_12075" "cell_12177" "cell_11653" "cell_10644" "cell_11993"
- [96] "cell_10322" "cell_11900" "cell_11315" "cell_10474" "cell_10480"
-[101] "cell_11220" "cell_10440" "cell_11596" "cell_10296" "cell_11856"
-[106] "cell_11728" "cell_10241" "cell_12016" "cell_11770" "cell_10917"
-[111] "cell_11805" "cell_12002" "cell_10599" "cell_10846" "cell_10687"
-[116] "cell_11330" "cell_11081" "cell_9953" "cell_10181" "cell_10395"
-[121] "cell_12021" "cell_11667" "cell_10547" "cell_11329" "cell_10332"
-[126] "cell_10562" "cell_11183" "cell_11138" "cell_10385" "cell_10125"
-[131] "cell_10047" "cell_10038" "cell_10386" "cell_11673" "cell_10105"
-[136] "cell_12162" "cell_10749" "cell_11549" "cell_11458" "cell_11290"
-[141] "cell_11213" "cell_10849" "cell_11465" "cell_9885" "cell_10416"
-[146] "cell_10847" "cell_11009" "cell_11733" "cell_10756" "cell_10479"
-[151] "cell_11260" "cell_11002" "cell_10117" "cell_10933" "cell_11840"
-[156] "cell_10922" "cell_11495" "cell_11380" "cell_10478" "cell_11026"
-[161] "cell_11880" "cell_11896" "cell_12110" "cell_11115" "cell_10559"
-[166] "cell_12151" "cell_11109" "cell_11014" "cell_11526" "cell_11018"
-[171] "cell_11582" "cell_11476" "cell_10065" "cell_10628" "cell_11603"
-[176] "cell_10825" "cell_9851" "cell_10634" "cell_10791" "cell_9844"
-[181] "cell_10886" "cell_11931" "cell_11975" "cell_11150" "cell_10450"
-[186] "cell_12115" "cell_11506" "cell_11239" "cell_11130" "cell_10011"
-[191] "cell_11922" "cell_11827" "cell_10393" "cell_11982" "cell_10229"
-[196] "cell_12140" "cell_9799" "cell_10907" "cell_11957" "cell_9784"
-[201] "cell_11204" "cell_10292" "cell_11229" "cell_10692" "cell_11370"
-[206] "cell_9972" "cell_10914" "cell_10027" "cell_10262" "cell_11657"
-[211] "cell_11552" "cell_11123" "cell_10900" "cell_11093" "cell_9778"
-[216] "cell_9938" "cell_11001" "cell_11619" "cell_12160" "cell_9876"
-[221] "cell_9776" "cell_10394" "cell_10029" "cell_11377" "cell_11679"
-[226] "cell_11054" "cell_11528" "cell_11913" "cell_11515" "cell_10435"
-[231] "cell_10758" "cell_10220" "cell_10624" "cell_11716" "cell_11371"
-[236] "cell_12042" "cell_10414" "cell_10828" "cell_10659" "cell_11424"
-[241] "cell_11096" "cell_12171" "cell_11803" "cell_11404" "cell_10561"
-[246] "cell_11180" "cell_10046" "cell_10009" "cell_9792" "cell_11853"
-[251] "cell_11095" "cell_11511" "cell_11835" "cell_11463" "cell_10146"
-[256] "cell_10317" "cell_11407" "cell_12173" "cell_10161" "cell_10438"
-[261] "cell_10981" "cell_10079" "cell_11210" "cell_11174" "cell_10876"
-[266] "cell_10087" "cell_11630" "cell_11434" "cell_9888" "cell_10367"
-[271] "cell_11107" "cell_11994" "cell_10192" "cell_11822" "cell_10647"
-[276] "cell_10436" "cell_11592" "cell_9817" "cell_11268" "cell_9961"
-[281] "cell_10071" "cell_9959" "cell_11419" "cell_10585" "cell_11214"
-[286] "cell_11084" "cell_11165" "cell_11327" "cell_11392" "cell_10718"
-[291] "cell_10466" "cell_12090" "cell_11555" "cell_10995" "cell_10526"
-[296] "cell_10761" "cell_11038" "cell_11232" "cell_10715" "cell_10458"
-[301] "cell_10019" "cell_10328" "cell_10411" "cell_10313" "cell_9930"
-[306] "cell_11114" "cell_9936" "cell_11234" "cell_10556" "cell_9846"
-[311] "cell_11871" "cell_11285" "cell_10991" "cell_11939" "cell_10213"
-[316] "cell_9863" "cell_11710" "cell_11256" "cell_10147" "cell_9989"
-[321] "cell_10464" "cell_10953" "cell_10388" "cell_10010" "cell_11485"
-[326] "cell_10695" "cell_11760" "cell_11328" "cell_11620" "cell_10694"
-[331] "cell_10175" "cell_9997" "cell_12147" "cell_10553" "cell_11266"
-[336] "cell_10467" "cell_11233" "cell_10963" "cell_12149" "cell_9986"
-[341] "cell_11276" "cell_11904" "cell_12179" "cell_9847" "cell_11303"
-[346] "cell_11299" "cell_10956" "cell_10347" "cell_11599" "cell_10697"
-[351] "cell_10190" "cell_10261" "cell_10498" "cell_11588" "cell_9977"
-[356] "cell_11839" "cell_11777" "cell_11941" "cell_10645" "cell_10833"
-[361] "cell_10672" "cell_10654" "cell_11024" "cell_10164" "cell_11522"
-[366] "cell_10407" "cell_12134" "cell_11056" "cell_11489" "cell_9969"
-[371] "cell_9820" "cell_11017" "cell_9835" "cell_12064" "cell_11562"
-[376] "cell_10345" "cell_10225" "cell_10783" "cell_12036" "cell_11333"
-[381] "cell_10812" "cell_10998" "cell_9892" "cell_10360" "cell_12152"
-[386] "cell_10508" "cell_9813" "cell_11124" "cell_11073" "cell_9859"
-[391] "cell_10421" "cell_10930" "cell_10374" "cell_12097" "cell_11217"
-[396] "cell_10800" "cell_11063" "cell_10363" "cell_10515" "cell_10267"
-[401] "cell_11047" "cell_11744" "cell_11564" "cell_9849" "cell_11916"
-[406] "cell_12082" "cell_12057" "cell_10664" "cell_11680" "cell_11542"
-[411] "cell_10765" "cell_12066" "cell_11438" "cell_12072" "cell_10441"
-[416] "cell_10396" "cell_10838" "cell_9832" "cell_10299" "cell_11402"
-[421] "cell_11736" "cell_11012" "cell_11484" "cell_11962" "cell_10604"
-[426] "cell_11966" "cell_10370" "cell_10099" "cell_10669" "cell_11774"
-[431] "cell_11579" "cell_10059" "cell_10511" "cell_10597" "cell_12031"
-[436] "cell_10961" "cell_10497" "cell_11934" "cell_11353" "cell_11133"
-[441] "cell_9837" "cell_11112" "cell_10272" "cell_10868" "cell_11734"
-[446] "cell_10554" "cell_11683" "cell_10898" "cell_10623" "cell_10864"
-[451] "cell_10217" "cell_10739" "cell_12174" "cell_12053" "cell_11859"
-[456] "cell_10103" "cell_12167" "cell_10848" "cell_9975" "cell_10204"
-[461] "cell_11678" "cell_10769" "cell_10369" "cell_10155" "cell_10860"
-[466] "cell_10512" "cell_10333" "cell_11149" "cell_10560" "cell_10510"
-[471] "cell_11658" "cell_10354" "cell_11141" "cell_11263" "cell_12058"
-[476] "cell_9856" "cell_11208" "cell_9779" "cell_11598" "cell_10231"
-[481] "cell_11547" "cell_10468" "cell_11961" "cell_10610" "cell_10453"
-[486] "cell_10048" "cell_11304" "cell_10571" "cell_11778" "cell_10546"
-[491] "cell_12111" "cell_11120" "cell_9940" "cell_12040" "cell_11471"
-[496] "cell_11470" "cell_11321" "cell_10236" "cell_11176" "cell_12094"
-[501] "cell_10509" "cell_10133" "cell_10359" "cell_11595" "cell_11019"
-[506] "cell_10602" "cell_11414" "cell_11838" "cell_11932" "cell_11057"
-[511] "cell_10303" "cell_10750" "cell_9880" "cell_10224" "cell_10885"
-[516] "cell_11281" "cell_10399" "cell_9816" "cell_10737" "cell_10250"
-[521] "cell_11040" "cell_9873" "cell_11782" "cell_10227" "cell_12125"
-[526] "cell_11714" "cell_11104" "cell_11354" "cell_10660" "cell_9907"
-[531] "cell_10249" "cell_10611" "cell_10018" "cell_11389" "cell_10098"
-[536] "cell_10401" "cell_11418" "cell_12092" "cell_10890" "cell_10850"
-[541] "cell_11791" "cell_11988" "cell_11897" "cell_10026" "cell_10403"
-[546] "cell_10030" "cell_11688" "cell_11571" "cell_10696" "cell_9974"
-[551] "cell_9967" "cell_11381" "cell_11972" "cell_12143" "cell_11837"
-[556] "cell_10521" "cell_11280" "cell_11694" "cell_10166" "cell_11010"
-[561] "cell_10947" "cell_11901" "cell_12044" "cell_10586" "cell_10428"
-[566] "cell_10115" "cell_11357" "cell_11121" "cell_12114" "cell_12076"
-[571] "cell_9823" "cell_11162" "cell_10836" "cell_11954" "cell_11713"
-[576] "cell_11168" "cell_10700" "cell_11845" "cell_11557" "cell_11346"
-[581] "cell_9962" "cell_11386" "cell_11799" "cell_10869" "cell_11411"
-[586] "cell_10766" "cell_11450" "cell_11058" "cell_10481" "cell_10123"
-[591] "cell_10238" "cell_10107" "cell_9968" "cell_11951" "cell_11811"
-[596] "cell_11519" "cell_11172" "cell_10661" "cell_10534" "cell_10904"
-[601] "cell_12081" "cell_10237" "cell_10247" "cell_10380" "cell_11199"
-[606] "cell_11447" "cell_11854" "cell_11524" "cell_10058" "cell_11586"
-[611] "cell_10234" "cell_11743" "cell_10256" "cell_11775" "cell_11270"
-[616] "cell_10089" "cell_9777" "cell_10635" "cell_10049" "cell_10410"
-[621] "cell_10675" "cell_10476" "cell_10832" "cell_10940" "cell_10788"
-[626] "cell_11818" "cell_11502" "cell_10731" "cell_12166" "cell_10646"
-[631] "cell_11397" "cell_10151" "cell_12085" "cell_11435" "cell_10239"
-[636] "cell_11715" "cell_12060" "cell_11798" "cell_9929" "cell_10189"
-[641] "cell_10212" "cell_9797" "cell_11529" "cell_11033" "cell_11794"
-[646] "cell_9812" "cell_9992" "cell_11696" "cell_10680" "cell_10319"
-[651] "cell_10120" "cell_10601" "cell_12145" "cell_10451" "cell_11243"
-[656] "cell_9824" "cell_11070" "cell_11983" "cell_11986" "cell_10422"
-[661] "cell_11664" "cell_10143" "cell_11368" "cell_11580" "cell_11583"
-[666] "cell_11312" "cell_11862" "cell_11493" "cell_11226" "cell_9785"
-[671] "cell_10417" "cell_9931" "cell_11277" "cell_11261" "cell_11642"
-[676] "cell_10977" "cell_10424" "cell_10588" "cell_9803" "cell_11938"
-[681] "cell_11877" "cell_10271" "cell_10177" "cell_10437" "cell_10741"
-[686] "cell_10580" "cell_11102" "cell_10945" "cell_11077" "cell_9916"
-[691] "cell_9861" "cell_10037" "cell_10485" "cell_10443" "cell_10140"
-[696] "cell_10285" "cell_11618" "cell_9845" "cell_11469" "cell_11140"
-[701] "cell_10452" "cell_10352" "cell_9894" "cell_11823" "cell_10944"
-[706] "cell_10488" "cell_10867" "cell_11516" "cell_12116" "cell_10755"
-[711] "cell_10072" "cell_11393" "cell_11650" "cell_10878" "cell_11400"
-[716] "cell_9868" "cell_10817" "cell_11700" "cell_11085" "cell_12007"
-[721] "cell_11998" "cell_12158" "cell_10315" "cell_10698" "cell_10471"
-[726] "cell_10111" "cell_11945" "cell_10999" "cell_11225" "cell_11083"
-[731] "cell_11539" "cell_12113" "cell_11158" "cell_9802" "cell_11173"
-[736] "cell_10034" "cell_10193" "cell_10831" "cell_12083" "cell_11296"
-[741] "cell_11007" "cell_10895" "cell_10725" "cell_11709" "cell_10626"
-[746] "cell_10168" "cell_9770" "cell_10870" "cell_10950" "cell_9924"
-[751] "cell_12006" "cell_9983" "cell_10787" "cell_10054" "cell_11118"
-[756] "cell_10732" "cell_10198" "cell_11923" "cell_10518" "cell_10418"
-[761] "cell_10484" "cell_10522" "cell_10153" "cell_11483" "cell_11309"
-[766] "cell_11445" "cell_11754" "cell_11914" "cell_10677" "cell_11772"
-[771] "cell_11697" "cell_9942" "cell_10202" "cell_10383" "cell_11074"
-[776] "cell_11212" "cell_10572" "cell_11342" "cell_10593" "cell_10283"
-[781] "cell_12056" "cell_9819" "cell_11771" "cell_11591" "cell_9998"
-[786] "cell_11144" "cell_11015" "cell_10381" "cell_10937" "cell_11265"
-[791] "cell_10086" "cell_10187" "cell_10215" "cell_11611" "cell_9911"
-[796] "cell_11308" "cell_10735" "cell_11978" "cell_11067" "cell_10491"
-[801] "cell_11003" "cell_10989" "cell_11480" "cell_10255" "cell_10312"
-[806] "cell_11548" "cell_11207" "cell_9920" "cell_10209" "cell_11211"
-[811] "cell_11422" "cell_11360" "cell_10305" "cell_10821" "cell_10461"
-[816] "cell_10008" "cell_10801" "cell_11319" "cell_10078" "cell_11651"
-[821] "cell_11287" "cell_10389" "cell_10135" "cell_10773" "cell_11246"
-[826] "cell_11623" "cell_11627" "cell_11031" "cell_10200" "cell_11113"
-[831] "cell_9794" "cell_12023" "cell_11197" "cell_11313" "cell_11129"
-[836] "cell_11597" "cell_9807" "cell_10095" "cell_11860"
-
-
-$`Spinal cord`
-$`Spinal cord`$aucThr
-$`Spinal cord`$aucThr$selected
-outlierOfGlobal
- 0.433
-
-$`Spinal cord`$aucThr$thresholds
- threshold nCells
-outlierOfGlobal 0.4333 0
-Global_k1 0.1939 239
-L_k2 0.1241 632
-R_k3 0.0913 754
-
-$`Spinal cord`$aucThr$comment
-[1] "The AUC might follow a normal distribution (random gene-set?). The right distribution is taller. "
-
-
-$`Spinal cord`$assignment
-character(0)
-```
+
:::
@@ -1893,7 +1003,7 @@ sce$leiden_clust <- clusterCells(sce, use.dimred = "PCA",
plotReducedDim(sce, "UMAP", color_by = "leiden_clust")
```
-
+
:::
:::
@@ -1922,7 +1032,7 @@ names(19): Allantois Cardiomyocytes ... Spinal cord Surface ectoderm
plotReducedDim(ref, dimred = "umap", color_by = "celltype")
```
-
+
``` r
# Repetitive work -> write a function
diff --git a/eda_qc.md b/eda_qc.md
index 3c13970..8c9294c 100644
--- a/eda_qc.md
+++ b/eda_qc.md
@@ -106,9 +106,9 @@ The distribution of total counts (called the unique molecular identifier or UMI
A simple approach would be to apply a threshold on the total count to only retain those barcodes with large totals. However, this may unnecessarily discard libraries derived from cell types with low RNA content.
::: callout
-Depending on your data source, identifying and discarding empty droplets may not be necessary. Some academic institutions have research cores dedicated to single cell work that perform the sample preparation and sequencing. Many of these cores will also perform empty droplet filtering and other initial QC steps. If the sequencing outputs were provided to you by someone else, make sure to communicate with them about what pre-processing steps have been performed, if any.
+Depending on your data source, identifying and discarding empty droplets may not be necessary. Some academic institutions have research cores dedicated to single cell work that perform the sample preparation and sequencing. Many of these cores will also perform empty droplet filtering and other initial QC steps. Specific details on the steps in common pipelines like [10x Genomics' CellRanger](https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials) can usually be found in the documentation that came with the sequencing material.
-
+The main point is: if the sequencing outputs were provided to you by someone else, make sure to communicate with them about what pre-processing steps have been performed, if any.
:::
:::: challenge
diff --git a/fig/cell_type_annotation-rendered-auc-dist2-1.png b/fig/cell_type_annotation-rendered-auc-dist2-1.png
new file mode 100644
index 0000000..e1e04a8
Binary files /dev/null and b/fig/cell_type_annotation-rendered-auc-dist2-1.png differ
diff --git a/fig/cell_type_annotation-rendered-unnamed-chunk-7-1.png b/fig/cell_type_annotation-rendered-unnamed-chunk-7-1.png
index f3ca7cb..73f876f 100644
Binary files a/fig/cell_type_annotation-rendered-unnamed-chunk-7-1.png and b/fig/cell_type_annotation-rendered-unnamed-chunk-7-1.png differ
diff --git a/fig/cell_type_annotation-rendered-unnamed-chunk-8-1.png b/fig/cell_type_annotation-rendered-unnamed-chunk-8-1.png
index 73f876f..82d3d6f 100644
Binary files a/fig/cell_type_annotation-rendered-unnamed-chunk-8-1.png and b/fig/cell_type_annotation-rendered-unnamed-chunk-8-1.png differ
diff --git a/intro-sce.md b/intro-sce.md
index a6f524d..db748cb 100644
--- a/intro-sce.md
+++ b/intro-sce.md
@@ -116,6 +116,17 @@ This class implements a data structure that stores all aspects of our single-cel
+:::: spoiler
+
+### Before `SingleCellExperiment`
+
+Before `SingleCellExperiment`, coders working with single cell data would sometimes keep all of these components in separate objects e.g. a matrix of counts, a data.frame of sample metadata, a data.frame of gene annotations and so on. There were two main disadvantages to this sort of "from scratch" approach:
+
+1. Tons of book-keeping. If you performed a QC step that removed dead cells, you also had to remember to remove that same set of cells from the cell-wise metadata. Un-expressed genes were dropped? Don't forget to filter the gene metadata table too.
+2. All the downstream steps had to be "from scratch" as well. All the data munging, analysis, and visualization code had to be customized to the idiosyncrasies of a given input set.
+
+::::
+
Let's look at an example dataset. `WTChimeraData` comes from a study on mouse development. We can assign one sample to a `SingleCellExperiment` object named `sce` like so:
@@ -261,7 +272,7 @@ Here we add a column called "conservation" that is just an integer sequence from
``` r
-rowData(sce)$conservation = 1:nrow(sce)
+rowData(sce)$conservation = rnorm(nrow(sce))
```
This is just a made-up example with a simple sequence of numbers, but in practice its convenient to store any sort of gene-wise information in the columns of the rowData.
@@ -384,21 +395,6 @@ altExpNames(0):
:::::::::::::::::::::::::::::::::::::::::::::
-:::: challenge
-
-#### Extension Challenge 1
-
-Before `SingleCellExperiment`, coders working with single cell data would sometimes keep all of these components in separate objects e.g. a matrix of counts, a data.frame of sample metadata, a data.frame of gene annotations and so on. What are the main disadvantages of this sort of "from scratch" approach?
-
-::: solution
-
-1. You have to do tons of book-keeping! If you perform a QC step that removes dead cells, now you also have to remember to remove that same set of cells from the cell-wise metadata. Dropped un-expressed genes? Don't forget to filter the gene metadata table too.
-
-2. All the downstream steps have to be "from scratch" as well! All the data munging, analysis, and visualization code has to be customized to the idiosyncrasies of your input. Agh!
-
-:::
-
-::::
:::::::::::::: checklist
diff --git a/md5sum.txt b/md5sum.txt
index ad41738..7ba160b 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -4,9 +4,9 @@
"config.yaml" "b0d664d3d6abdd0e98b16282e1c03107" "site/built/config.yaml" "2024-09-24"
"index.md" "495939ddd3f110be3bbcd49b60f4a7ce" "site/built/index.md" "2024-09-24"
"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-09-24"
-"episodes/intro-sce.Rmd" "709fc538c9872b9494fa37f1059ea4a0" "site/built/intro-sce.md" "2024-10-02"
-"episodes/eda_qc.Rmd" "b4800ddfe2d5deb5047311658f254e6d" "site/built/eda_qc.md" "2024-10-02"
-"episodes/cell_type_annotation.Rmd" "5bd585c6e4c6fc09a7443ce4da35899f" "site/built/cell_type_annotation.md" "2024-10-02"
+"episodes/intro-sce.Rmd" "b704934867b22d804de1e0fa0a9600eb" "site/built/intro-sce.md" "2024-10-02"
+"episodes/eda_qc.Rmd" "b21851ec0c9912dd9cb8a0cf230bcf9d" "site/built/eda_qc.md" "2024-10-02"
+"episodes/cell_type_annotation.Rmd" "8fab6e0cbb60d6fe6a67a0004c5ce5ab" "site/built/cell_type_annotation.md" "2024-10-02"
"episodes/multi-sample.Rmd" "4711a38fd8b29961424215dd17fb7528" "site/built/multi-sample.md" "2024-09-30"
"episodes/large_data.Rmd" "f19fa53e9e63d4cb8fe0f6ab61c8fc3a" "site/built/large_data.md" "2024-10-02"
"episodes/hca.Rmd" "3f2af9dc9e53fd617512a37db87f20a7" "site/built/hca.md" "2024-10-02"