mgatk: mitochondrial genome analysis toolkit
☆114Jan 20, 2025Updated last year
Alternatives and similar repositories for mgatk
Users that are interested in mgatk are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome☆22Jun 10, 2022Updated 4 years ago
- Mitochondrial Alteration Enrichment and Genome Analysis Toolkit☆24Jan 16, 2024Updated 2 years ago
- Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020☆22Jul 13, 2023Updated 2 years ago
- ☆13Apr 16, 2021Updated 5 years ago
- Single-Cell Genotyping Tool☆218Oct 2, 2023Updated 2 years ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- ☆16Jul 9, 2024Updated last year
- Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome☆223Feb 4, 2026Updated 4 months ago
- Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR☆115Dec 18, 2025Updated 6 months ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆435May 11, 2026Updated last month
- Code repository for the Tumor Immune Cell Atlas (TICA) project☆66Mar 31, 2022Updated 4 years ago
- CONICS: COpy-Number analysis In single-Cell RNA-Sequencing☆77Feb 27, 2023Updated 3 years ago
- R package for semi-supervised single-cell data integration☆99Jan 27, 2026Updated 4 months ago
- Analysis of cell-cell communication at single-cell resolution☆107Sep 10, 2024Updated last year
- Efficient genotyping bi-allelic SNPs on single cells☆162Oct 30, 2025Updated 7 months ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Repo for scripts for Ludwig et al mtDNA genotyping☆16Nov 22, 2019Updated 6 years ago
- CellRank: dynamics from multi-view single-cell data☆454Jun 9, 2026Updated last week
- Clone identification from single-cell data☆65Nov 10, 2022Updated 3 years ago
- Pileup biallelic SNPs from single-cell and bulk RNA-seq data☆84Jun 9, 2022Updated 4 years ago
- kallisto index tag extractor☆19Jul 6, 2019Updated 6 years ago
- Tools for single-cell data processing☆135May 27, 2024Updated 2 years ago
- STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data☆183Dec 18, 2021Updated 4 years ago
- Identify major cellular signals in bulk transcriptomes☆11Jun 1, 2022Updated 4 years ago
- Extracts fastq reads for specified barcode(s) from one or multiple FASTQ files☆13Jan 31, 2016Updated 10 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- ☆12Nov 9, 2022Updated 3 years ago
- Flexible, probablistic metrics for quality control of scRNA-seq data☆22May 27, 2026Updated 3 weeks ago
- A software package for detection of copy number alterations from tumor samples☆12May 8, 2015Updated 11 years ago
- A tool for detecting somatic variants in single cell data☆222Sep 15, 2024Updated last year
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆401May 6, 2026Updated last month
- In this study, we perform systematic comparative analysis of seven widely-used SNV-calling methods, including SAMtools, the GATK Best Pra…☆16Oct 16, 2019Updated 6 years ago
- Cell type specific enrichments using finemapped variants and quantitative epigenetic data☆49Sep 1, 2023Updated 2 years ago
- dandelion - A single cell BCR/TCR V(D)J-seq analysis package☆127Jun 11, 2026Updated last week
- A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction☆99Jun 9, 2026Updated last week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- RNA Velocity generalized through dynamical modeling☆505Feb 25, 2026Updated 3 months ago
- Convert between AnnData and SingleCellExperiment☆151Updated this week
- zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs☆295Jul 12, 2024Updated last year
- Information-based dimensionality reduction☆30Dec 14, 2024Updated last year
- Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of …☆21Aug 28, 2025Updated 9 months ago
- cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data☆147Apr 5, 2024Updated 2 years ago
- Trajectory Inference Based on SNP information.☆24Jun 19, 2024Updated last year