satijalab/seurat

R toolkit for single cell genomics

JGCRI/gcam-core

GCAM -- The Global Change Analysis Model

sqjin/CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

benjjneb/dada2

Accurate sample inference from amplicon data with single nucleotide resolution

rstudio/renv

renv: Project environments for R.

jokergoo/ComplexHeatmap

Make Complex Heatmaps

stuart-lab/signac

R toolkit for the analysis of single-cell chromatin data

joey711/phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

r-spatial/sf

Simple Features for R

rstudio/shiny

Easy interactive web applications with R

rstudio/rmarkdown

Dynamic Documents for R

Rdatatable/data.table

R's data.table package extends data.frame:

GreenleafLab/ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

YuLab-SMU/clusterProfiler

📊 A universal enrichment tool for interpreting omics data

prisma-flowdiagram/PRISMA2020

Produce PRISMA-2020 compliant flow diagrams

cole-trapnell-lab/monocle3

tidyverse/ggplot2

An implementation of the Grammar of Graphics in R

chris-mcginnis-ucsf/DoubletFinder

R package for detecting doublets in single-cell RNA sequencing data

tidyverse/dplyr

dplyr: A grammar of data manipulation