satijalab/seurat

R toolkit for single cell genomics

stuart-lab/signac

R toolkit for the analysis of single-cell chromatin data

sqjin/CellChat

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

broadinstitute/infercnv

Inferring CNV from Single-Cell RNA-Seq

tidyverse/dplyr

dplyr: A grammar of data manipulation

tidyverse/ellmer

Call LLM APIs from R

YuLab-SMU/clusterProfiler

📊 A universal enrichment tool for interpreting omics data

jokergoo/ComplexHeatmap

Make Complex Heatmaps

cole-trapnell-lab/monocle3

tidyverse/ggplot2

An implementation of the Grammar of Graphics in R

kassambara/ggpubr

'ggplot2' Based Publication Ready Plots

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

mojaveazure/seurat-disk

Interfaces for HDF5-based Single Cell File Formats

r-spatial/sf

Simple Features for R

rstudio/rmarkdown

Dynamic Documents for R

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:

rstudio/reticulate

R Interface to Python

rdpeng/ProgrammingAssignment2

Repository for Programming Assignment 2 for R Programming on Coursera