broadinstitute/infercnv

Inferring CNV from Single-Cell RNA-Seq

satijalab/seurat

R toolkit for single cell genomics

cole-trapnell-lab/monocle3

stuart-lab/signac

R toolkit for the analysis of single-cell chromatin data

saeyslab/nichenetr

NicheNet: predict active ligand-target links between interacting cells

YuLab-SMU/clusterProfiler

📊 A universal enrichment tool for interpreting omics data

kassambara/ggpubr

'ggplot2' Based Publication Ready Plots

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:

sqjin/CellChat

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

immunogenomics/harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

r-spatial/sf

Simple Features for R

JGCRI/gcam-core

GCAM -- The Global Change Analysis Model