| bioconductor-methylkit | 1.32.1 | DNA methylation analysis from high-throughput bisulfite sequencing results | Mar 27, 2025 | Artistic-2.0 |
| r-libra | 1.0.0 | Libra is an R package to identify differentially expressed genes in single-cell data, accounting for biological replicates. | Jun 2, 2025 | GPL-3 |
| r-muscadet | 0.2.1 | Identification of copy number alterations (CNAs) in cancer cells from single-cell multiomics data. | Feb 23, 2026 | GPL-3 |
| r-numbat | 1.3.2_1 | A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>. | Mar 25, 2025 | MIT |
| r-remapenrich | 0.99.0 | Bioinformatics tools to compute statistical enrichment of geonomic regions for ReMap peaks | Mar 25, 2025 | AGPL-3 |
| r-scistreer | 1.2.0 | Fast maximum-likelihood phylogeny inference from noisy single-cell data using the 'ScisTree' algorithm by Yufeng Wu (2019) <doi:10.1093/bioinformatics/btz676>. 'scistreer' provides an 'R' interface and improves speed via 'Rcpp' and 'RcppParallel', making the method applicable to massive single-cell datasets (>10,000 cells). | Mar 25, 2025 | GPL-3 |
| r-seuratdata | 0.2.1 | Single cell RNA sequencing datasets can be large, consisting of matrices that contain expression data for several thousand features across several thousand cells. This package is designed to easily install, manage, and learn about various single-cell datasets, provided Seurat objects and distributed as independent packages. | Mar 25, 2025 | GPL-3 |
