diff --git a/README.md b/README.md index 8cfab2a..81266f3 100755 --- a/README.md +++ b/README.md @@ -7,17 +7,17 @@ Single cell RNA-seq (scRNA-seq) captures the transcriptomic phenotype of multipl ## Prerequisites -Install all required R packages in the R_requirement.txt files using either bioconductor or CRAN +Install all required R packages in the [R_requirement.txt](resources/R_requirement.txt) files using either bioconductor or CRAN ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") -BiocManager::install(R_requirement.txt) +BiocManager::install("package") ``` or ``` -install.packages(R_requirement.txt) +install.packages("package") ``` ## Data availability @@ -91,7 +91,7 @@ we can further clean up our dataset by removing clusters 2 (CCL3, CCL4 cluster), ## Versioning -We use Seurat V3.1.2 edgeR V3.20.9 under R V3.5.1. on Northwestern High Performance Computing Cluster +We use Seurat V3.1.2 and edgeR V3.20.9 under R V3.5.1 on Northwestern High Performance Computing Cluster. Detail session info can be found [here](resources/sessioninfo.txt). ## Authors diff --git a/resources/R_requirement.txt b/resources/R_requirement.txt new file mode 100644 index 0000000..3605d5b --- /dev/null +++ b/resources/R_requirement.txt @@ -0,0 +1,3 @@ +Seurat 3.1.2 +edgeR 3.20.9 +pheatmap 1.0.10 \ No newline at end of file diff --git a/resources/sessioninfo.txt b/resources/sessioninfo.txt new file mode 100644 index 0000000..95fb0fc --- /dev/null +++ b/resources/sessioninfo.txt @@ -0,0 +1,39 @@ +R version 3.5.1 (2018-07-02) +Platform: x86_64-pc-linux-gnu (64-bit) +Running under: Red Hat Enterprise Linux Server 7.5 (Maipo) + +Matrix products: default +BLAS: /hpc/software/R/3.5.1/lib64/R/lib/libRblas.so +LAPACK: /hpc/software/R/3.5.1/lib64/R/lib/libRlapack.so + +locale: + [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 + [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C +[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C + +attached base packages: +[1] grid stats graphics grDevices utils datasets methods base + +other attached packages: +[1] Seurat_3.1.2 ComplexHeatmap_2.3.2 + +loaded via a namespace (and not attached): + [1] TH.data_1.0-10 Rtsne_0.15 colorspace_1.4-1 rjson_0.2.20 ggridges_0.5.2 circlize_0.4.8 + [7] GlobalOptions_0.1.1 clue_0.3-57 rstudioapi_0.10 farver_2.0.3 leiden_0.3.2 listenv_0.8.0 + [13] npsurv_0.4-0 ggrepel_0.8.1 mvtnorm_1.0-12 codetools_0.2-15 splines_3.5.1 R.methodsS3_1.7.1 + [19] mnormt_1.5-5 lsei_1.2-0 TFisher_0.2.0 jsonlite_1.6.1 ica_1.0-2 cluster_2.0.7-1 + [25] png_0.1-7 R.oo_1.23.0 uwot_0.1.6 sctransform_0.2.1 compiler_3.5.1 httr_1.4.1 + [31] assertthat_0.2.1 Matrix_1.2-14 lazyeval_0.2.2 htmltools_0.4.0 tools_3.5.1 rsvd_1.0.2 + [37] igraph_1.2.4.2 gtable_0.3.0 glue_1.3.1 RANN_2.6.1 reshape2_1.4.3 dplyr_0.8.4 + [43] rappdirs_0.3.1 Rcpp_1.0.3 Biobase_2.42.0 vctrs_0.2.2 multtest_2.38.0 gdata_2.18.0 + [49] ape_5.3 nlme_3.1-137 gbRd_0.4-11 lmtest_0.9-37 stringr_1.4.0 globals_0.12.5 + [55] lifecycle_0.1.0 irlba_2.3.3 gtools_3.8.1 future_1.16.0 MASS_7.3-50 zoo_1.8-7 + [61] scales_1.1.0 parallel_3.5.1 sandwich_2.5-1 RColorBrewer_1.1-2 reticulate_1.14 pbapply_1.4-2 + [67] gridExtra_2.3 ggplot2_3.2.1 stringi_1.4.5 mutoss_0.1-12 plotrix_3.7-7 caTools_1.17.1.1 + [73] BiocGenerics_0.28.0 bibtex_0.4.2.2 shape_1.4.4 Rdpack_0.11-1 SDMTools_1.1-221.2 rlang_0.4.4 + [79] pkgconfig_2.0.3 bitops_1.0-6 lattice_0.20-35 ROCR_1.0-5 purrr_0.3.3 labeling_0.3 + [85] htmlwidgets_1.5.1 cowplot_1.0.0 tidyselect_1.0.0 RcppAnnoy_0.0.14 plyr_1.8.5 magrittr_1.5 + [91] R6_2.4.1 gplots_3.0.0 multcomp_1.4-12 pillar_1.4.3 sn_1.5-5 fitdistrplus_1.0-14 + [97] survival_2.42-3 tsne_0.1-3 tibble_2.1.3 future.apply_1.4.0 crayon_1.3.4 KernSmooth_2.23-15 +[103] plotly_4.9.1 GetoptLong_0.1.8 data.table_1.12.8 metap_1.3 digest_0.6.23 tidyr_1.0.2 +[109] numDeriv_2016.8-1.1 R.utils_2.9.2 RcppParallel_4.4.4 stats4_3.5.1 munsell_0.5.0 viridisLite_0.3.0 \ No newline at end of file