Package: epidecodeR 1.21.0

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_1.21.0.tar.gz
epidecodeR_1.21.0.zip(r-4.7)epidecodeR_1.21.0.zip(r-4.6)epidecodeR_1.21.0.zip(r-4.5)
epidecodeR_1.21.0.tgz(r-4.6-any)epidecodeR_1.21.0.tgz(r-4.5-any)
epidecodeR_1.21.0.tar.gz(r-4.7-any)epidecodeR_1.21.0.tar.gz(r-4.6-any)
epidecodeR_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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-1.21.0(bioc 3.24)epidecodeR-1.20.0(bioc 3.23)

differentialexpression generegulation histonemodification functionalprediction transcription geneexpression epitranscriptomics epigenetics functionalgenomics systemsbiology transcriptomics chiponchip differential-expression genomics genomics-visualization

4.70 score 5 stars 7 scripts 9 exports 121 dependencies

Last updated from:3dff80ab09. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	204
linux-devel-x86_64	OK	380
source / vignettes	OK	303
linux-release-x86_64	OK	382
macos-release-arm64	OK	263
macos-oldrel-arm64	OK	214
windows-devel	OK	303
windows-release	OK	317
windows-oldrel	OK	286
wasm-release	OK	210

Exports:epidecodeR get_empirical_table get_eventcounts get_grpcounts get_grptables get_signtest get_theoretical_table makeplot plot_test

Dependencies:abind askpass backports BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops boot broom car carData cigarillo cli codetools colorspace corrplot cowplot cpp11 crayon curl DelayedArray Deriv doBy dplyr EnvStats farver forecast formatR Formula fracdiff futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv mime minqa modelr nlme nloptr nnet nortest numDeriv openssl pbkrtest pillar pkgconfig polynom purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack reformulas restfulr Rhtslib rjson rlang Rsamtools rstatix rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray SparseM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite withr XML XVector yaml zoo

epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation

Rendered fromepidecodeR.Rmdusingknitr::rmarkdown

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

Help page	Topics
Analysis function for generating epidecodeR object. This function distributes dysregulated genes into user defined groups and calculates cumulative probabilities and ANOVA test statistics for significance testing in difference of log2FC means between groups of dysregulated genes	epidecodeR
epidecodeR object - a S4 class object	epidecodeR-class
get_empirical_table method	get_empirical_table get_empirical_table,epidecodeR-method
get_eventcounts method	get_eventcounts get_eventcounts,epidecodeR-method
get_grpcounts method	get_grpcounts get_grpcounts,epidecodeR-method
get_grptables method	get_grptables get_grptables,epidecodeR-method
get_signtest method	get_signtest get_signtest,epidecodeR-method
get_theoretical_table method	get_theoretical_table get_theoretical_table,epidecodeR-method
Generate CDF plot using epidecodeR object generated using epidecodeR function	makeplot
Generates boxplot of distribution of log2FC of dysregulated genes and adjusted P value of signficance test of difference in mean log2FC between groups computed using one-way ANOVA test	plot_test

Package: epidecodeR 1.21.0

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

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