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New NCBI to AnnData tutorial #4480

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Dec 13, 2023
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6ac1f10
init NCBI to AnnData tutorial
hexhowells Oct 23, 2023
94c9ee2
add introduction and initial descriptions
hexhowells Oct 24, 2023
e189f93
add more information
hexhowells Oct 25, 2023
6cd049a
Merge branch 'galaxyproject:main' into NCBI-to-AnnData
hexhowells Oct 25, 2023
219d645
update tutorial
hexhowells Nov 3, 2023
b458fc8
Merge branch 'galaxyproject:main' into NCBI-to-AnnData
hexhowells Nov 3, 2023
0c96981
Merge branch 'NCBI-to-AnnData' of https://github.com/hexhowells/train…
hexhowells Nov 3, 2023
6e2e685
fix linting issues
hexhowells Nov 3, 2023
2c7175f
add bibliography
hexhowells Nov 10, 2023
2f5567a
update tutorial
hexhowells Nov 10, 2023
ac64076
updated tutorial
hexhowells Nov 10, 2023
9b0ac04
Update topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.md
hexhowells Nov 10, 2023
7e760ea
Update topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.md
hexhowells Nov 10, 2023
d98ae6d
Update topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.md
hexhowells Nov 10, 2023
c32381b
include all 10 samples in example image
hexhowells Nov 10, 2023
660ae61
Update tool version
hexhowells Nov 10, 2023
270fc05
update replicate tool parameters
hexhowells Nov 10, 2023
bdd9b65
add comment box about parameter usage
hexhowells Nov 19, 2023
ba5707c
Remove introduction header
hexhowells Nov 20, 2023
f01aa1c
Indent block quote to match item
hexhowells Nov 21, 2023
d02b778
add Choose Your Own Tutorial section
hexhowells Nov 21, 2023
a3e3747
testing this commit works
nomadscientist Nov 30, 2023
6a78a2c
Revert "testing this commit works"
nomadscientist Nov 30, 2023
3b27cd6
minor intro text updates
nomadscientist Nov 30, 2023
e55ebba
changing import to avoid downloading locally
nomadscientist Nov 30, 2023
4e7add4
finish data import shift
nomadscientist Nov 30, 2023
1c2210d
fix icon
nomadscientist Nov 30, 2023
3a273a7
Update _config.yml
nomadscientist Nov 30, 2023
d6c2d3e
Update _config.yml
nomadscientist Nov 30, 2023
12eae9c
fix yml
nomadscientist Nov 30, 2023
4f7f926
add final icon in data ingest section
nomadscientist Nov 30, 2023
8d0848a
icon fix
nomadscientist Nov 30, 2023
5e6f6a1
Icon updates
nomadscientist Nov 30, 2023
c13ac10
add tagging info
nomadscientist Nov 30, 2023
21f3dd8
Merge branch 'NCBI-to-AnnData' of https://github.com/hexhowells/train…
nomadscientist Nov 30, 2023
a6cb0e1
icon change
nomadscientist Nov 30, 2023
184872f
fix zenodo links
nomadscientist Nov 30, 2023
b5a7e41
selector is not coloured right
nomadscientist Nov 30, 2023
7b9ebfa
update datatype conversions
nomadscientist Nov 30, 2023
ce21825
add param-files icons
nomadscientist Nov 30, 2023
7b2676c
minor fix
nomadscientist Nov 30, 2023
53487ee
Update _config.yml
nomadscientist Nov 30, 2023
4cd3179
fix manipulate section
nomadscientist Nov 30, 2023
32cfc01
Update tutorial.md
nomadscientist Nov 30, 2023
f8c23a3
minor text edits
nomadscientist Nov 30, 2023
c1d2530
fix grammar
nomadscientist Nov 30, 2023
169f4ed
more details icon
nomadscientist Nov 30, 2023
7e32d85
remove default tool options
nomadscientist Dec 1, 2023
fc2e065
minor text edits
nomadscientist Dec 1, 2023
2c4560d
Update topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.md
hexhowells Dec 12, 2023
315a310
Update topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.md
hexhowells Dec 12, 2023
fc40054
Update topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.md
hexhowells Dec 12, 2023
774294d
left align table
hexhowells Dec 12, 2023
9561836
add explanation of NCBI database
hexhowells Dec 12, 2023
1cd21b6
add screenshot of cell metadata
hexhowells Dec 12, 2023
cd3728b
add workflow
pavanvidem Dec 12, 2023
3f3c8fb
add more detail about finding metadata
hexhowells Dec 12, 2023
ce4296b
Merge branch 'NCBI-to-AnnData' of https://github.com/hexhowells/train…
hexhowells Dec 12, 2023
e59c559
add details about replicate files
hexhowells Dec 12, 2023
12536a6
fix typos
hexhowells Dec 12, 2023
d482a13
Update topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.md
hexhowells Dec 13, 2023
a5579e7
Fix linting error
hexhowells Dec 13, 2023
5503254
Update to a working worflow and change test files type to tabular
pavanvidem Dec 13, 2023
8622962
Update editors and testers; also added links to workflow and example …
pavanvidem Dec 13, 2023
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1 change: 1 addition & 0 deletions _config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -102,6 +102,7 @@ icon-tag:
event: far fa-calendar
feedback: far fa-comments
galaxy-advanced-search: fas fa-angle-double-down
galaxy-show-active: fa fa-map-marker
galaxy-barchart: fas fa-chart-bar
galaxy-bug: fas fa-bug
galaxy-chart-select-data: fas fa-database
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13 changes: 13 additions & 0 deletions topics/single-cell/tutorials/scrna-ncbi-anndata/tutorial.bib
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
@article{Song2022,
title = {Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states},
volume = {13},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-021-27322-4},
DOI = {10.1038/s41467-021-27322-4},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Song, Hanbing and Weinstein, Hannah N. W. and Allegakoen, Paul and Wadsworth, Marc H. and Xie, Jamie and Yang, Heiko and Castro, Ethan A. and Lu, Kevin L. and Stohr, Bradley A. and Feng, Felix Y. and Carroll, Peter R. and Wang, Bruce and Cooperberg, Matthew R. and Shalek, Alex K. and Huang, Franklin W.},
year = {2022},
month = jan
}
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