satijalab/seurat

R toolkit for single cell genomics

jinworks/CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

sqjin/CellChat

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

r-spatial/sf

Simple Features for R

tidyverse/dplyr

dplyr: A grammar of data manipulation

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

benjjneb/dada2

Accurate sample inference from amplicon data with single nucleotide resolution

rstudio/renv

renv: Project environments for R.

cole-trapnell-lab/monocle3

posit-dev/skills

A collection of Claude Skills from Posit

scverse/anndataR

AnnData interoperability in R

broadinstitute/infercnv

Inferring CNV from Single-Cell RNA-Seq

stuart-lab/signac

R toolkit for the analysis of single-cell chromatin data

rstudio/shiny

Easy interactive web applications with R

hadley/r4ds

R for data science: a book

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:

JGCRI/gcam-core

GCAM -- The Global Change Analysis Model

YuLab-SMU/clusterProfiler

📊 A universal enrichment tool for interpreting omics data