Source code used in the paper : The transcription factor NFIL3 drives ILC specification from lymphoid progenitors
Léger J, Artano E, Coulais D, Belletoise N, Fadhloun R, Kenney D, Bhandoola A, Harly C.
This repository contains scripts and resources used to perform DNase-seq, Bulk RNA-seq, scRNA-seq and CUT&RUN post-processing analyzes.
Information about pre-processing steps are detailed in PRE-PROCESSING.md.
Complete explanation is avaible (https://github.com/JosephLeger/NFIL3_dev_ILC/Full_Tutorial/).
> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C LC_TIME=French_France.1252
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] VennDiagram_1.7.3 futile.logger_1.4.3 igraph_1.3.5
[4] slingshot_2.2.1 TrajectoryUtils_1.2.0 SingleCellExperiment_1.16.0
[7] princurve_2.1.6 Nebulosa_1.4.0 patchwork_1.1.2
[10] simspec_0.0.0.9000 SeuratObject_4.1.3 Seurat_4.3.0
[13] EnhancedVolcano_1.12.0 ggrepel_0.9.2 org.Mm.eg.db_3.14.0
[16] AnnotationDbi_1.56.2 edgeR_3.36.0 limma_3.50.3
[19] sva_3.35.2 BiocParallel_1.28.3 genefilter_1.76.0
[22] mgcv_1.8-39 nlme_3.1-155 pheatmap_1.0.12
[25] ggfortify_0.4.17 tximport_1.22.0 Hmisc_4.7-2
[28] Formula_1.2-4 survival_3.2-13 lattice_0.20-45
[31] forcats_0.5.2 stringr_1.5.0 dplyr_1.0.10
[34] purrr_0.3.5 readr_2.1.3 tidyr_1.2.1
[37] tibble_3.3.0 ggplot2_3.4.0 tidyverse_1.3.2
[40] DiffBind_3.4.11 SummarizedExperiment_1.24.0 Biobase_2.54.0
[43] MatrixGenerics_1.6.0 matrixStats_0.63.0 GenomicRanges_1.46.1
[46] GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.4
[49] BiocGenerics_0.40.0
loaded via a namespace (and not attached):
[1] rtracklayer_1.54.0 scattermore_0.8 coda_0.19-4 bit64_4.0.5
[5] knitr_1.41 irlba_2.3.5.1 DelayedArray_0.20.0 data.table_1.14.6
[9] rpart_4.1.16 hwriter_1.3.2.1 KEGGREST_1.34.0 RCurl_1.98-1.9
[13] generics_0.1.3 lambda.r_1.2.4 cowplot_1.1.1 RSQLite_2.2.18
[17] RANN_2.6.1 future_1.29.0 bit_4.0.5 tzdb_0.3.0
[21] spatstat.data_3.0-0 xml2_1.3.3 lubridate_1.9.0 httpuv_1.6.6
[25] assertthat_0.2.1 gargle_1.2.1 amap_0.8-19 apeglm_1.16.0
[29] xfun_0.35 hms_1.1.2 promises_1.2.0.1 restfulr_0.0.15
[33] caTools_1.18.2 dbplyr_2.2.1 readxl_1.4.1 DBI_1.1.3
[37] htmlwidgets_1.5.4 spatstat.geom_3.0-3 googledrive_2.0.0 ellipsis_0.3.2
[41] ks_1.14.0 backports_1.4.1 annotate_1.72.0 deldir_1.0-6
[45] vctrs_0.5.1 ROCR_1.0-11 abind_1.4-5 cachem_1.0.6
[49] withr_2.5.0 BSgenome_1.62.0 progressr_0.11.0 bdsmatrix_1.3-6
[53] checkmate_2.1.0 sctransform_0.3.5 GenomicAlignments_1.30.0 mclust_6.0.0
[57] goftest_1.2-3 cluster_2.1.2 lazyeval_0.2.2 crayon_1.5.2
[61] spatstat.explore_3.0-5 pkgconfig_2.0.3 vipor_0.4.5 nnet_7.3-17
[65] rlang_1.1.6 globals_0.16.2 lifecycle_1.0.3 miniUI_0.1.1.1
[69] extrafontdb_1.0 modelr_0.1.10 invgamma_1.1 polyclip_1.10-4
[73] ggrastr_1.0.1 cellranger_1.1.0 lmtest_0.9-40 Matrix_1.5-3
[77] ashr_2.2-54 zoo_1.8-11 reprex_2.0.2 base64enc_0.1-3
[81] beeswarm_0.4.0 ggridges_0.5.4 googlesheets4_1.0.1 png_0.1-8
[85] viridisLite_0.4.1 rjson_0.2.21 bitops_1.0-7 KernSmooth_2.23-20
[89] Biostrings_2.62.0 blob_1.2.3 mixsqp_0.3-48 SQUAREM_2021.1
[93] spatstat.random_3.0-1 ShortRead_1.52.0 parallelly_1.32.1 jpeg_0.1-10
[97] scales_1.2.1 memoise_2.0.1 magrittr_2.0.3 plyr_1.8.8
[101] ica_1.0-3 gplots_3.1.3 zlibbioc_1.40.0 compiler_4.1.3
[105] BiocIO_1.4.0 bbmle_1.0.25 RColorBrewer_1.1-3 ash_1.0-15
[109] fitdistrplus_1.1-8 Rsamtools_2.10.0 cli_3.4.1 systemPipeR_2.0.8
[113] XVector_0.34.0 listenv_0.8.0 pbapply_1.6-0 formatR_1.12
[117] htmlTable_2.4.1 MASS_7.3-55 tidyselect_1.2.0 stringi_1.7.8
[121] proj4_1.0-12 emdbook_1.3.13 yaml_2.3.6 locfit_1.5-9.6
[125] latticeExtra_0.6-30 tools_4.1.3 timechange_0.1.1 future.apply_1.10.0
[129] parallel_4.1.3 rstudioapi_0.14 foreign_0.8-82 gridExtra_2.3
[133] Rtsne_0.16 digest_0.6.30 pracma_2.4.2 shiny_1.7.3
[137] Rcpp_1.0.9 broom_1.0.1 ggalt_0.4.0 later_1.3.0
[141] RcppAnnoy_0.0.20 httr_1.4.4 colorspace_2.0-3 tensor_1.5
[145] rvest_1.0.3 XML_3.99-0.13 fs_1.5.2 reticulate_1.26
[149] truncnorm_1.0-9 splines_4.1.3 uwot_0.1.14 spatstat.utils_3.0-1
[153] sp_1.5-1 plotly_4.10.1 xtable_1.8-4 futile.options_1.0.1
[157] jsonlite_1.8.3 R6_2.5.1 pillar_1.10.2 htmltools_0.5.3
[161] mime_0.12 glue_1.8.0 fastmap_1.1.0 codetools_0.2-18
[165] maps_3.4.1 GreyListChIP_1.26.0 mvtnorm_1.1-3 spatstat.sparse_3.0-0
[169] numDeriv_2016.8-1.1 ggbeeswarm_0.6.0 leiden_0.4.3 gtools_3.9.4
[173] Rttf2pt1_1.3.11 interp_1.1-3 munsell_0.5.0 GenomeInfoDbData_1.2.7
[177] haven_2.5.1 reshape2_1.4.4 gtable_0.3.1 extrafont_0.18