Package: epidecodeR 1.13.0

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_1.13.0.tar.gz
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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'))

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

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

bioconductor-package

9 exports 0.49 score 109 dependencies

Last updated 2 months agofrom:32a3738795

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 BiocGenerics BiocIO BiocParallel Biostrings bitops boot broom car carData cli codetools colorspace corrplot cowplot cpp11 crayon curl DelayedArray dplyr EnvStats fansi farver formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle lme4 magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv mime minqa munsell nlme nloptr nnet nortest numDeriv openssl pbkrtest pillar pkgconfig polynom purrr quantreg R6 RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang Rsamtools rstatix rtracklayer S4Arrays S4Vectors scales snow SparseArray SparseM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml zlibbioc

epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation

Rendered fromepidecodeR.Rmdusingknitr::rmarkdownon Jun 23 2024.

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 1.13.0

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

epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation

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