Tools
We develop and maintain freely available, open source software implementations of genomic data science tools.
Featured
![RAMEN](https://github.com/ErickNavarroD/RAMEN/raw/master/man/figures/logo.png)
Regional Association of Methylome variability with the Exposome and geNome
![vmrseq](https://github.com/nshen7/vmrseq/raw/main/man/figures/method.png)
R package for detecting variably methylated regions (VMRs) from single-cell methylation sequencing
![bayesDCA](https://github.com/giulianonetto/bayesdca/raw/master/man/figures/README-unnamed-chunk-7-1.png)
R package to Perform Bayesian Decision Curve Analysis for clinical prediction models and diagnostic tests
![dmrseq](https://github.com/kdkorthauer/dmrseq/raw/master/inst/sticker/dmrseq.png)
an R/Bioconductor package for differential methylation analysis using bulk whole genome bisulfite sequencing data
![scDD](https://github.com/Bioconductor/BiocStickers/raw/devel/scDD/scDD.png)
an R/Bioconductor package for differential distribution analysis using single-cell RNA-sequencing data
![benchmarkfdr-shiny](https://github.com/kdkorthauer/benchmarkfdr-shiny/raw/master/img/screenshot2.png)
R/Shiny application for exploring results from “A practical guide to methods controlling false discoveries in computational biology”
More
![benchmarkfdrData2019](https://media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-019-1716-1/MediaObjects/13059_2019_1716_Fig6_HTML.png)
R/Bioconductor Experiment Package containing benchmark results from “A practical guide to methods controlling false discoveries in computational biology”
![SingleCellExperiment](https://github.com/Bioconductor/BiocStickers/raw/devel/SingleCellExperiment/SingleCellExperiment.png)
an R/Bioconductor package defining S4 Classes for storing Single Cell Data
![scDDboost](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10275512/bin/nihms-1901161-f0003.jpg)
an R package to analyze changes in the distribution of single-cell expression data between two experimental conditions with multiple cell types
![oligoGames](https://raw.githubusercontent.com/cshukla/cshukla.github.io/master/assets/img/oligoGames.synopsis.jpg)
an R package for the analysis of tiled massively parallel reporter assays (MPRAs)
Legacy
![MADGiC](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426832/bin/btu858f1p.jpg)
R package for the identification of cancer driver genes by integrating somatic mutation, expression, replication timing, and functional impact