Package: epidecodeR 1.15.0

Kandarp Joshi

epidecodeR: epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation

epidecodeR is a package capable of analysing impact of degree of DNA/RNA epigenetic chemical modifications on dysregulation of genes or proteins. This package integrates chemical modification data generated from a host of epigenomic or epitranscriptomic techniques such as ChIP-seq, ATAC-seq, m6A-seq, etc. and dysregulated gene lists in the form of differential gene expression, ribosome occupancy or differential protein translation and identify impact of dysregulation of genes caused due to varying degrees of chemical modifications associated with the genes. epidecodeR generates cumulative distribution function (CDF) plots showing shifts in trend of overall log2FC between genes divided into groups based on the degree of modification associated with the genes. The tool also tests for significance of difference in log2FC between groups of genes.

Authors:Kandarp Joshi [aut, cre], Dan Ohtan Wang [aut]

epidecodeR_1.15.0.tar.gz
epidecodeR_1.15.0.zip(r-4.5)epidecodeR_1.15.0.zip(r-4.4)epidecodeR_1.15.0.zip(r-4.3)
epidecodeR_1.15.0.tgz(r-4.4-any)epidecodeR_1.15.0.tgz(r-4.3-any)
epidecodeR_1.15.0.tar.gz(r-4.5-noble)epidecodeR_1.15.0.tar.gz(r-4.4-noble)
epidecodeR_1.15.0.tgz(r-4.4-emscripten)epidecodeR_1.15.0.tgz(r-4.3-emscripten)
epidecodeR.pdf |epidecodeR.html✨
epidecodeR/json (API)

# Install 'epidecodeR' in R:
install.packages('epidecodeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kandarprj/epidecoder/issues

On BioConductor:epidecodeR-1.15.0(bioc 3.21)epidecodeR-1.14.0(bioc 3.20)

differentialexpressiongeneregulationhistonemodificationfunctionalpredictiontranscriptiongeneexpressionepitranscriptomicsepigeneticsfunctionalgenomicssystemsbiologytranscriptomicschiponchipdifferential-expressiongenomicsgenomics-visualization

4.70 score 5 stars 1 scripts 194 downloads 9 exports 116 dependencies

Last updated 4 months agofrom:787612bbd0. Checks:7 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-winOKJan 28 2025
R-4.5-linuxOKJan 28 2025
R-4.4-winOKJan 28 2025
R-4.4-macOKJan 28 2025
R-4.3-winOKJan 28 2025
R-4.3-macOKJan 28 2025

Exports:epidecodeRget_empirical_tableget_eventcountsget_grpcountsget_grptablesget_signtestget_theoretical_tablemakeplotplot_test

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsbootbroomcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11crayoncurlDelayedArrayDerivdoBydplyrEnvStatsfansifarverformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnortestnumDerivopensslpbkrtestpillarpkgconfigpolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppEigenRCurlRdpackreformulasrestfulrRhtslibrjsonrlangRsamtoolsrstatixrtracklayerS4ArraysS4VectorsscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation

Rendered fromepidecodeR.Rmdusingknitr::rmarkdownon Jan 28 2025.

Last update: 2021-03-25
Started: 2021-03-18