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
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epidecodeR_1.15.0.tgz(r-4.4-any)epidecodeR_1.15.0.tgz(r-4.3-any)
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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'))

Peer review:

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

On BioConductor:epidecodeR-1.13.0(bioc 3.20)epidecodeR-1.12.0(bioc 3.19)

differentialexpressiongeneregulationhistonemodificationfunctionalpredictiontranscriptiongeneexpressionepitranscriptomicsepigeneticsfunctionalgenomicssystemsbiologytranscriptomicschiponchipdifferential-expressiongenomicsgenomics-visualization

4.70 score 5 stars 1 scripts 140 downloads 9 exports 114 dependencies

Last updated 23 days agofrom:787612bbd0. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:epidecodeRget_empirical_tableget_eventcountsget_grpcountsget_grptablesget_signtestget_theoretical_tablemakeplotplot_test

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsbootbroomcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11crayoncurlDelayedArrayDerivdoBydplyrEnvStatsfansifarverformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnortestnumDerivopensslpbkrtestpillarpkgconfigpolynompurrrquantregR6RColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsrstatixrtracklayerS4ArraysS4VectorsscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc

epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation

Rendered fromepidecodeR.Rmdusingknitr::rmarkdownon Oct 30 2024.

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