Repository containing all the scripts and code necessary for generating the results in the manuscript Uncovering functional lncRNAs by scRNA-seq with ELATUS.
Some of the scRNA-seq datasets included in the manuscript are quite computationally heavy to process. Therefore a HPC with enough memory, cores and RAM is required to end-to-end reproduce all the results.
The different analysis have been performed on the following systems:
- Linux: CentOS 7.15.1804
- Cell Ranger 3.0.1
- STAR 2.7.9
- Kallisto 0.46.1
- Bustools 0.40.0
- Salmon 1.4.0
- Kallisto 0.46.2 (pulmonary fibrotic dataset only)
- Cell Ranger 5.0.1 (single-cell multiome only)
install.packages("Seurat")
install.packages("patchwork")
install.packages("ggplot2")
install.packages("RColorBrewer")
install.packages("cluster")
install.packages("UpSetR")
install.packages("ggpubr")
install.packages("reshape")
BiocManager::install("tximport")
BiocManager::install("scran")
BiocManager::install("scater")
BiocManager::install("SingleCellExperiment")
BiocManager::install("BUSpaRse")
BiocManager::install("DropletUtils")
BiocManager::install("scDblFinder")
BiocManager::install("scRNAseq")
install.packages("Signac")
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /beegfs/easybuild/CentOS/7.5.1804/Skylake/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib64/libflexiblas.so.3.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Signac_1.9.0 reshape_0.8.9
[3] scDblFinder_1.8.0 ggpubr_0.4.0
[5] scRNAseq_2.8.0 UpSetR_1.4.0
[7] cluster_2.1.4 RColorBrewer_1.1-3
[9] DropletUtils_1.14.2 BUSpaRse_1.8.0
[11] scater_1.22.0 scran_1.22.1
[13] scuttle_1.4.0 SingleCellExperiment_1.16.0
[15] SummarizedExperiment_1.24.0 Biobase_2.54.0
[17] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
[19] IRanges_2.28.0 S4Vectors_0.32.4
[21] BiocGenerics_0.40.0 MatrixGenerics_1.6.0
[23] matrixStats_0.62.0 ggplot2_3.4.2
[25] tximport_1.22.0 patchwork_1.1.2
[27] SeuratObject_4.1.3 Seurat_4.0.1
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 rtracklayer_1.54.0
[3] scattermore_0.8 R.methodsS3_1.8.2
[5] tidyr_1.2.1 bit64_4.0.5
[7] irlba_2.3.5.1 DelayedArray_0.20.0
[9] R.utils_2.12.0 data.table_1.14.2
[11] rpart_4.1.16 KEGGREST_1.34.0
[13] RCurl_1.98-1.9 AnnotationFilter_1.18.0
[15] generics_0.1.3 GenomicFeatures_1.46.5
[17] ScaledMatrix_1.2.0 cowplot_1.1.1
[19] RSQLite_2.2.18 RANN_2.6.1
[21] future_1.28.0 bit_4.0.4
[23] spatstat.data_3.0-0 xml2_1.3.3
[25] httpuv_1.6.6 assertthat_0.2.1
[27] viridis_0.6.2 hms_1.1.2
[29] promises_1.2.0.1 fansi_1.0.3
[31] restfulr_0.0.15 progress_1.2.2
[33] dbplyr_2.2.1 igraph_1.3.5
[35] DBI_1.1.3 htmlwidgets_1.5.4
[37] spatstat.geom_3.0-6 purrr_1.0.2
[39] ellipsis_0.3.2 backports_1.4.1
[41] dplyr_1.0.10 biomaRt_2.50.3
[43] deldir_1.0-6 sparseMatrixStats_1.6.0
[45] vctrs_0.6.5 ensembldb_2.18.4
[47] ROCR_1.0-11 abind_1.4-5
[49] cachem_1.0.6 withr_2.5.0
[51] BSgenome_1.62.0 progressr_0.11.0
[53] sctransform_0.3.5 GenomicAlignments_1.30.0
[55] prettyunits_1.1.1 goftest_1.2-3
[57] ExperimentHub_2.2.1 lazyeval_0.2.2
[59] crayon_1.5.2 edgeR_3.36.0
[61] pkgconfig_2.0.3 nlme_3.1-160
[63] vipor_0.4.5 ProtGenerics_1.26.0
[65] rlang_1.1.1 globals_0.16.1
[67] lifecycle_1.0.3 miniUI_0.1.1.1
[69] filelock_1.0.2 BiocFileCache_2.2.1
[71] rsvd_1.0.5 AnnotationHub_3.2.2
[73] polyclip_1.10-0 lmtest_0.9-40
[75] Matrix_1.5-1 carData_3.0-5
[77] Rhdf5lib_1.16.0 zoo_1.8-11
[79] beeswarm_0.4.0 ggridges_0.5.4
[81] png_0.1-7 viridisLite_0.4.1
[83] rjson_0.2.21 bitops_1.0-7
[85] R.oo_1.25.0 KernSmooth_2.23-20
[87] rhdf5filters_1.6.0 Biostrings_2.62.0
[89] blob_1.2.3 DelayedMatrixStats_1.16.0
[91] stringr_1.4.1 parallelly_1.32.1
[93] spatstat.random_3.1-3 rstatix_0.7.0
[95] ggsignif_0.6.3 beachmat_2.10.0
[97] scales_1.2.1 memoise_2.0.1
[99] magrittr_2.0.3 plyr_1.8.7
[101] ica_1.0-3 zlibbioc_1.40.0
[103] compiler_4.1.2 dqrng_0.3.0
[105] BiocIO_1.4.0 fitdistrplus_1.1-8
[107] Rsamtools_2.10.0 cli_3.6.2
[109] XVector_0.34.0 listenv_0.8.0
[111] pbapply_1.5-0 MASS_7.3-58.1
[113] mgcv_1.8-40 tidyselect_1.2.0
[115] stringi_1.7.8 yaml_2.3.5
[117] BiocSingular_1.10.0 locfit_1.5-9.6
[119] ggrepel_0.9.1 grid_4.1.2
[121] fastmatch_1.1-3 tools_4.1.2
[123] future.apply_1.9.1 parallel_4.1.2
[125] bluster_1.4.0 metapod_1.2.0
[127] gridExtra_2.3 plyranges_1.14.0
[129] Rtsne_0.16 digest_0.6.29
[131] BiocManager_1.30.19 shiny_1.7.2
[133] Rcpp_1.0.9 car_3.1-0
[135] broom_1.0.1 BiocVersion_3.14.0
[137] later_1.3.0 RcppAnnoy_0.0.20
[139] httr_1.4.4 AnnotationDbi_1.56.2
[141] colorspace_2.0-3 XML_3.99-0.11
[143] tensor_1.5 reticulate_1.26
[145] splines_4.1.2 RcppRoll_0.3.0
[147] uwot_0.1.14 statmod_1.4.37
[149] spatstat.utils_3.0-1 sp_1.5-0
[151] xgboost_1.6.0.1 plotly_4.10.0
[153] xtable_1.8-4 jsonlite_1.8.2
[155] zeallot_0.1.0 R6_2.5.1
[157] pillar_1.8.1 htmltools_0.5.3
[159] mime_0.12 glue_1.6.2
[161] fastmap_1.1.0 BiocParallel_1.28.3
[163] BiocNeighbors_1.12.0 interactiveDisplayBase_1.32.0
[165] codetools_0.2-18 utf8_1.2.2
[167] lattice_0.20-45 spatstat.sparse_3.0-0
[169] tibble_3.1.8 curl_4.3.3
[171] ggbeeswarm_0.6.0 leiden_0.4.3
[173] survival_3.4-0 limma_3.50.3
[175] munsell_0.5.0 rhdf5_2.38.1
[177] GenomeInfoDbData_1.2.7 HDF5Array_1.22.1
[179] reshape2_1.4.4 gtable_0.3.1
[181] spatstat.core_2.4-4