Publication-quality sequence logos in R

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

Network construction, analysis, and comparison for microbial compositional data

Single-cell epigenomics analysis tools

Qiita - A multi-omics databasing effort

Single-nuclei RNA-seq and ATAC-seq in Alzheimer's disease

A tool for semi-automatic cell type classification

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

A Framework for Building Robust Shiny Apps

RStudio add-in to make plots interactively with ggplot2

Visualize microbiome data with black magic ggtree

Collection of various algorithms implemented in R.

Efficient R programming: a book

Statistical Analysis of Network Data with R, 2nd Edition

Publication quality NGS track plotting

A package to help convert different single-cell data formats to each other

Metagenomics Analysis Tools

Visual self-service analytics platform for big omics data.

Reference mapping for single-cell genomics

List of papers on deconvolution of cell types in bulk RNA-seq based on single-cell signatures

CellRank: dynamics from multi-view single-cell data

Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM function.

Combination matrix axis for 'ggplot2' to create 'UpSet' plots

A novel unsupervised batch removal framework, called iMAP, based on neural networks.

A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.

List of software packages for multi-omics analysis

A reference-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles