singleCellTK 2.10.1
The Single Cell Toolkit (SCTK) is an interactive scRNA-Seq analysis package that allows a user to upload raw scRNA-Seq count matrices and perform downstream scRNA-Seq analysis interactively through a web interface, or through a set of R functions through the command line. The package is written in R with a graphical user interface (GUI) written in Shiny. Users can perform analysis with modules for conducting quality control, clustering, batch correction, differential expression, pathway enrichment, and sample size calculator, all in a simple to use point and click interface. The toolkit also supports command line data processing, and results can be loaded into the GUI for additional exploration and downstream analysis.
Due to the range of features that are available in SCTK, we have prepared several vignettes to help you get started, which are all available at https://www.camplab.net/sctk/
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: AlmaLinux 8.8 (Sapphire Caracal)
##
## Matrix products: default
## BLAS: /share/pkg.7/r/4.2.1/install/lib64/R/lib/libRblas.so
## LAPACK: /share/pkg.7/r/4.2.1/install/lib64/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [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] BiocStyle_2.24.0 singleCellTK_2.10.1
## [3] DelayedArray_0.22.0 Matrix_1.6-1
## [5] SingleCellExperiment_1.18.0 SummarizedExperiment_1.26.1
## [7] Biobase_2.56.0 GenomicRanges_1.48.0
## [9] GenomeInfoDb_1.32.2 IRanges_2.30.0
## [11] S4Vectors_0.34.0 BiocGenerics_0.42.0
## [13] MatrixGenerics_1.8.0 matrixStats_0.62.0
##
## loaded via a namespace (and not attached):
## [1] softImpute_1.4-1 pbapply_1.5-0
## [3] lattice_0.20-45 GSVA_1.44.2
## [5] vctrs_0.6.3 fastICA_1.2-3
## [7] usethis_2.1.6 mgcv_1.8-40
## [9] GSVAdata_1.34.0 blob_1.2.3
## [11] survival_3.3-1 spatstat.data_3.0-1
## [13] later_1.3.0 R.utils_2.11.0
## [15] DBI_1.1.3 rappdirs_0.3.3
## [17] uwot_0.1.16 dqrng_0.3.0
## [19] jpeg_0.1-9 enrichR_3.0
## [21] zlibbioc_1.42.0 htmlwidgets_1.5.4
## [23] mvtnorm_1.1-3 GlobalOptions_0.1.2
## [25] future_1.26.1 inline_0.3.19
## [27] leiden_0.4.2 multipanelfigure_2.1.2
## [29] parallel_4.2.1 scater_1.24.0
## [31] irlba_2.3.5 Rcpp_1.0.8.3
## [33] KernSmooth_2.23-20 DT_0.23
## [35] promises_1.2.0.1 limma_3.52.2
## [37] pkgload_1.2.4 magick_2.7.3
## [39] graph_1.74.0 RcppParallel_5.1.5
## [41] Hmisc_4.7-0 startupmsg_0.9.6
## [43] assertive.types_0.0-3 fs_1.5.2
## [45] brio_1.1.3 basilisk_1.10.2
## [47] mnormt_2.1.0 digest_0.6.29
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## [59] iterators_1.0.14 DropletUtils_1.16.0
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## [63] circlize_0.4.15 spam_2.8-0
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## [67] GetoptLong_1.0.5 xfun_0.31
## [69] zoo_1.8-10 tidyselect_1.1.2
## [71] reshape2_1.4.4 purrr_0.3.4
## [73] ica_1.0-2 viridisLite_0.4.0
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## [89] M3Drop_1.24.0 httpuv_1.6.5
## [91] assertive.base_0.0-9 TH.data_1.1-1
## [93] BiocNeighbors_1.14.0 annotate_1.74.0
## [95] MCMCprecision_0.4.0 jsonlite_1.8.0
## [97] XVector_0.36.0 bit_4.0.4
## [99] mime_0.12 gridExtra_2.3
## [101] gplots_3.1.3 Rsamtools_2.12.0
## [103] assertive.properties_0.0-5 stringi_1.7.6
## [105] processx_3.6.1 distr_2.8.0
## [107] spatstat.sparse_3.0-2 rbibutils_2.2.8
## [109] scattermore_0.8 spatstat.explore_3.2-1
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## [127] scran_1.24.0 locfit_1.5-9.5
## [129] zellkonverter_1.8.0 scDblFinder_1.12.0
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## [133] gridGraphics_0.5-1 R.oo_1.25.0
## [135] dbplyr_2.2.0 sessioninfo_1.2.2
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## [139] munsell_0.5.0 R.methodsS3_1.8.2
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## [153] parallelly_1.32.0 ResidualMatrix_1.6.0
## [155] AnnotationHub_3.6.0 RANN_2.6.1
## [157] aplot_0.1.10 SeuratObject_4.1.3
## [159] ggtree_3.6.2 BiocIO_1.6.0
## [161] celldex_1.8.0 RcppAnnoy_0.0.19
## [163] goftest_1.2-3 patchwork_1.1.0.9000
## [165] tibble_3.1.7 cluster_2.1.3
## [167] future.apply_1.9.0 Seurat_4.3.0.1
## [169] tidytree_0.4.2 ellipsis_0.3.2
## [171] prettyunits_1.1.1 ggridges_0.5.3
## [173] shinyalert_3.0.0 mclust_5.4.10
## [175] igraph_1.3.2 multtest_2.52.0
## [177] RcppEigen_0.3.3.9.2 shinyjs_2.1.0
## [179] remotes_2.4.2 TFisher_0.2.0
## [181] scMerge_1.14.0 basilisk.utils_1.10.0
## [183] testthat_3.1.4 spatstat.utils_3.0-3
## [185] htmltools_0.5.2 BiocFileCache_2.4.0
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## [189] GenomicFeatures_1.48.3 loo_2.5.1
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## [193] interactiveDisplayBase_1.36.0 XML_3.99-0.10
## [195] foreign_0.8-82 withr_2.5.0
## [197] scuttle_1.6.2 fitdistrplus_1.1-8
## [199] BiocParallel_1.30.3 xgboost_1.6.0.1
## [201] bit64_4.0.5 multcomp_1.4-19
## [203] foreach_1.5.2 ProtGenerics_1.28.0
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## [209] rsvd_1.0.5 ScaledMatrix_1.4.0
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## [225] scds_1.14.0 cachem_1.0.6
## [227] desc_1.4.1 interp_1.1-2
## [229] deldir_1.0-6 dir.expiry_1.6.0
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## [233] metapod_1.4.0 ggplot2_3.4.2
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## [237] shinycssloaders_1.0.0 clue_0.3-61
## [239] rprojroot_2.0.3 tools_4.2.1
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## [243] magrittr_2.0.3 RCurl_1.98-1.7
## [245] proxy_0.4-27 ape_5.6-2
## [247] ggplotify_0.1.1 xml2_1.3.3
## [249] rmarkdown_2.14 httr_1.4.3
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## [297] scales_1.2.0 filelock_1.0.2
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## [301] hms_1.1.1 Rtsne_0.16
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