Package: DEFormats 1.35.0

Andrzej Oleś

DEFormats: Differential gene expression data formats converter

Convert between different data formats used by differential gene expression analysis tools.

Authors:Andrzej Oleś

DEFormats_1.35.0.tar.gz
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DEFormats.pdf |DEFormats.html✨
DEFormats/json (API)
NEWS

# Install 'DEFormats' in R:

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

Bug tracker:https://github.com/aoles/deformats/issues

On BioConductor:DEFormats-1.33.0(bioc 3.20)DEFormats-1.32.0(bioc 3.19)

immunooncology differentialexpression geneexpression rnaseq sequencing transcription

6.79 score 4 stars 1 packages 74 scripts 414 downloads 5 exports 72 dependencies

Last updated 18 days agofrom:05370ad991. Checks:OK: 5 NOTE: 2. 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	OK	Oct 30 2024
R-4.4-mac	OK	Oct 30 2024
R-4.3-win	OK	Oct 30 2024
R-4.3-mac	OK	Oct 30 2024

Exports:as.DESeqDataSet as.DGEList DGEList simulateNormFactors simulateRnaSeqData

Dependencies:abind askpass backports BH Biobase BiocGenerics BiocParallel checkmate cli codetools colorspace cpp11 crayon curl data.table DelayedArray DESeq2 edgeR fansi farver formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig R6 RColorBrewer Rcpp RcppArmadillo rlang S4Arrays S4Vectors scales snow SparseArray statmod SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Differential gene expression data formats converter

Andrzej Oleś

Rendered fromDEFormats.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2018-02-07
Started: 2016-03-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert to DESeqDataSet	as.DESeqDataSet as.DESeqDataSet.DGEList
Convert to DGEList	as.DGEList as.DGEList.DESeqDataSet
Convert Between Differential Gene Expression Data Formats	DEFormats
DGEList Constructor Generic	DGEList DGEList,RangedSummarizedExperiment-method
Simulate Normalization Factors	simulateNormFactors
Example counts table of RNA-seq data	simulateRnaSeqData

Usage by other packages (reverse dependencies)