Package: csdR 1.13.3

Jakob Peder Pettersen

csdR: Differential gene co-expression

This package contains functionality to run differential gene co-expression across two different conditions. The algorithm is inspired by Voigt et al. 2017 and finds Conserved, Specific and Differentiated genes (hence the name CSD). This package include efficient and variance calculation by bootstrapping and Welford's algorithm.

Authors:Jakob Peder Pettersen [aut, cre]

csdR_1.13.3.tar.gz
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csdR.pdf |csdR.html✨
csdR/json (API)
NEWS

# Install 'csdR' in R:

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

Bug tracker:https://github.com/almaaslab/csdr/issues

Pkgdown site:https://almaaslab.github.io

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

normal_expression - Sample expression matrices for CSD
sick_expression - Sample expression matrices for CSD

On BioConductor:csdR-1.13.3(bioc 3.21)csdR-1.12.0(bioc 3.20)

differentialexpression graphandnetwork geneexpression network cpp openmp

4.85 score 7 stars 7 scripts 154 downloads 3 exports 105 dependencies

Last updated 4 months agofrom:0df2dbcd14. Checks:6 OK, 3 ERROR. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 06 2025
R-4.5-win-x86_64	ERROR	Feb 06 2025
R-4.5-linux-x86_64	OK	Feb 06 2025
R-4.4-win-x86_64	OK	Feb 06 2025
R-4.4-mac-x86_64	OK	Feb 06 2025
R-4.4-mac-aarch64	OK	Feb 06 2025
R-4.3-win-x86_64	ERROR	Feb 06 2025
R-4.3-mac-x86_64	ERROR	Feb 06 2025
R-4.3-mac-aarch64	OK	Feb 06 2025

Exports:partial_argsort run_cor_bootstrap run_csd

Dependencies:AnnotationDbi askpass backports base64enc Biobase BiocGenerics Biostrings bit bit64 blob bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI digest doParallel dynamicTreeCut evaluate fansi farver fastcluster fastmap fontawesome foreach foreign Formula fs generics GenomeInfoDb GenomeInfoDbData ggplot2 glue GO.db gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr impute IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lattice lifecycle magrittr MASS Matrix matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr png preprocessCore R6 rappdirs RColorBrewer Rcpp RhpcBLASctl rlang rmarkdown rpart RSQLite rstudioapi S4Vectors sass scales stringi stringr survival sys tibble tinytex UCSC.utils utf8 vctrs viridis viridisLite WGCNA withr xfun XVector yaml

Analyzing differential co-expression with csdR

Rendered fromcsdR.Rmdusingknitr::rmarkdownon Feb 06 2025.

Last update: 2024-11-07
Started: 2021-06-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Sample expression matrices for CSD	data-expression normal_expression sick_expression
Extract indecies corresponding to the largest elements	partial_argsort
Run bootstrapping of Spearman correlations within a dataset	run_cor_bootstrap
Run CSD analysis	run_csd