Easily generate information-rich, publication-quality tables from R

Useful bash one-liners for bioinformatics.

Aggregate results from bioinformatics analyses across many samples into a single report.

📊 Circular and Rectangular Manhattan Plot

A quality control analysis tool for high throughput sequencing data

A library for creating complex UpSet plots with ggplot2 geoms

Consistent adapter and quality trimming for NGS, with extra functionality for RRBS data

Publication-ready volcano plots with enhanced colouring and labeling

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

Pretty heatmaps

🎯 ChIP peak Annotation, Comparison and Visualization

R data package for annotating/converting Gene IDs

Visualizing transcript structure and annotation using ggplot2

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing

Allele-specific alignment sorting

An R interface to the MEME Suite

Devel repository for bsseq

Reduce + Visualize Gene Ontology

Genomic Association Tester

Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrapped ranges (bootRanges), or set of control ranges that are matched across one …

Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=annotatr.

API for HOMER in R for Genomic Analysis using Tidy Conventions

R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms

Code to reproduce analysis in "Addressing confounding artifacts in reconstruction of gene co-expression networks"

Cluster-based analysis of CpG methylation

An R package for weighted region comethylation network analysis

Scripts for accessing revigo gene ontology plots from R

A pipeline to identify differentially-methylated regions from whole-genome bisulfite sequencing data

R-package for GO-enrichment analyses