Tools

RAMEN

Regional Association of Methylome variability with the Exposome and geNome

vmrseq

R package for detecting variably methylated regions (VMRs) from single-cell methylation sequencing

bayesDCA

R package to Perform Bayesian Decision Curve Analysis for clinical prediction models and diagnostic tests

dmrseq

an R/Bioconductor package for differential methylation analysis using bulk whole genome bisulfite sequencing data

scDD

an R/Bioconductor package for differential distribution analysis using single-cell RNA-sequencing data

benchmarkfdr-shiny

R/Shiny application for exploring results from “A practical guide to methods controlling false discoveries in computational biology”

benchmarkfdrData2019

R/Bioconductor Experiment Package containing benchmark results from “A practical guide to methods controlling false discoveries in computational biology”

SingleCellExperiment

an R/Bioconductor package defining S4 Classes for storing Single Cell Data

scDDboost

an R package to analyze changes in the distribution of single-cell expression data between two experimental conditions with multiple cell types

oligoGames

an R package for the analysis of tiled massively parallel reporter assays (MPRAs)

MADGiC

R package for the identification of cancer driver genes by integrating somatic mutation, expression, replication timing, and functional impact