Package: consensusDE 1.25.0

Ashley J. Waardenberg

consensusDE: RNA-seq analysis using multiple algorithms

This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq". It uses RUV-seq (optional) to remove unwanted sources of variation.

Authors:Ashley J. Waardenberg [aut, cre], Martha M. Cooper [ctb]

consensusDE_1.25.0.tar.gz
consensusDE_1.25.0.zip(r-4.5)consensusDE_1.25.0.zip(r-4.4)consensusDE_1.25.0.zip(r-4.3)
consensusDE_1.25.0.tgz(r-4.4-any)consensusDE_1.25.0.tgz(r-4.3-any)
consensusDE_1.25.0.tar.gz(r-4.5-noble)consensusDE_1.25.0.tar.gz(r-4.4-noble)
consensusDE_1.25.0.tgz(r-4.4-emscripten)consensusDE_1.25.0.tgz(r-4.3-emscripten)
consensusDE.pdf |consensusDE.html✨
consensusDE/json (API)
NEWS

# Install 'consensusDE' in R:

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

On BioConductor:consensusDE-1.23.0(bioc 3.20)consensusDE-1.22.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

transcriptomics multiplecomparison clustering sequencing software

4.00 score 10 scripts 170 downloads 3 exports 140 dependencies

Last updated 23 days agofrom:44f18e03c1. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 30 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 30 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	NOTE	Oct 30 2024
R-4.3-mac	NOTE	Oct 31 2024

Exports:buildSummarized diag_plots multi_de_pairs

Dependencies:abind airway AnnotationDbi AnnotationFilter aroma.light askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cli codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dendextend DESeq2 digest dplyr EDASeq edgeR EnsDb.Hsapiens.v86 ensembldb fansi farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable hms httr httr2 hwriter interp IRanges isoband jpeg jsonlite KEGGREST labeling lambda.r lattice latticeExtra lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl org.Hs.eg.db pcaMethods pillar pkgconfig plogr png prettyunits progress ProtGenerics purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer RUVSeq S4Arrays S4Vectors scales ShortRead snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect TxDb.Dmelanogaster.UCSC.dm3.ensGene UCSC.utils utf8 vctrs viridis viridisLite withr XML xml2 XVector yaml zlibbioc

consensusDE: DE analysis using multiple algorithms

Ashley J. Waardenberg

Rendered fromconsensusDE.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2019-12-03
Started: 2018-09-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Generate summarized Read File for DE analyses	buildSummarized
QC/diagnostic plotting	diag_plots
Batch - multiDE analysis of many comparisons	multi_de_pairs