Package: SCdeconR 1.0.1

SCdeconR: Deconvolution of Bulk RNA-Seq Data using Single-Cell RNA-Seq Data as Reference

Streamlined workflow from deconvolution of bulk RNA-seq data to downstream differential expression and gene-set enrichment analysis. Provide various visualization functions.

Authors:Yuanhang Liu [aut, cre]

SCdeconR_1.0.1.tar.gz
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SCdeconR_1.0.1.tgz(r-4.4-any)SCdeconR_1.0.1.tgz(r-4.3-any)
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SCdeconR.pdf |SCdeconR.html✨
SCdeconR/json (API)
NEWS

# Install 'SCdeconR' in R:

install.packages('SCdeconR', repos = c('https://liuy12.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/liuy12/scdeconr/issues

Datasets:

ffpemodel - Relationship between average tpm and ffpe artifacts based on a gam model

On CRAN:

bulk-rna-seq-deconvolution deconvolution differential-expression ffpe geneset-enrichment-analysis scdeconr single-cell

19 exports 2 stars 1.33 score 184 dependencies 4 scripts 192 downloads

Last updated 4 months agofrom:6ea77b43d5. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Aug 28 2024
R-4.5-win	WARNING	Aug 28 2024
R-4.5-linux	WARNING	Aug 28 2024
R-4.4-win	WARNING	Aug 28 2024
R-4.4-mac	WARNING	Aug 28 2024
R-4.3-win	WARNING	Aug 28 2024
R-4.3-mac	WARNING	Aug 28 2024

Exports:bulk_generator celltype_expression comparedeg_scatter comparegsea_scatter compute_metrics construct_ref gsea_heatmap gsea_rwplot gsea_sumplot load_scdata prepare_rnk prop_barplot read_gmt reformat_gmt run_de scaling scdecon transformation write_gmt

Dependencies:abind askpass base64enc beachmat BH Biobase BiocGenerics BiocManager bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table DelayedArray DelayedMatrixStats deldir digest doParallel dotCall64 dplyr dqrng edgeR evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome foreach fs future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggrepel ggridges glmGamPoi globals glue goftest gplots gridBase gridExtra gtable gtools harmony HDF5Array here highr htmltools htmlwidgets httpuv httr ica igraph IRanges irlba isoband iterators jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval leiden lifecycle limma listenv lmtest locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI munsell nlme NMF openssl parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML registry reshape2 reticulate rhdf5 rhdf5filters Rhdf5lib RhpcBLASctl rlang rmarkdown rngtools ROCR rprojroot RSpectra Rtsne S4Arrays S4Vectors sass scales scattermore sctransform Seurat SeuratObject shiny SingleCellExperiment sitmo sourcetools sp spam SparseArray sparseMatrixStats spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils statmod stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tinytex UCSC.utils utf8 uwot vctrs viridisLite withr xfun xtable XVector yaml zlibbioc zoo

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Generate artificial bulk RNA-seq samples based on simulation	bulk_generator
Compute cell type specific gene expression	celltype_expression
Generate a scatter plot comparing two differential expression results	comparedeg_scatter
Generate a scatter plot comparing two gene set enrichment analysis results	comparegsea_scatter
Statistical evaluations of predicted cell proportions	compute_metrics
Integration of single-cell/nuclei RNA-seq data as reference	construct_ref
relationship between average tpm and ffpe artifacts based on a gam model	ffpemodel
Heatmap to demonstrate enrichment of selected gene-sets	gsea_heatmap
GSEA random-walk plot	gsea_rwplot
Summary plot of gene set enrichment analysis	gsea_sumplot
Load, filter and normalize scRNA-seq/snRNA-seq data	load_scdata
Prepare .rnk file for GSEA preranked analysis	prepare_rnk
Bar plot of cell type proportions across samples	prop_barplot
Methods to manipulate .gmt files	read_gmt reformat_gmt write_gmt
Differential expression analysis	run_de
Normalization of gene expression data	scaling
Deconvolution of bulk RNA-seq data	scdecon
Transformation of gene expression data	transformation