328 Open source projects that are alternatives of or similar to mgatk

Bead-based single-cell atac processing

Inference of switch-like differential expression along single-cell trajectories

Spark VCF data source implementation for Dataframes

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

CUT&RUN and CUT&Tag data processing and analysis

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

A tool for semi-automatic cell type annotation

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Numerical Encoding for Human Genetic Variants

A tool to plot significant regions of GWAS

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

A package for designing activity-informed nucleic acid diagnostics for viruses.

Transcripts annotation and GO enrichment Fisher tests

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Multiome GRN inference.

Bioconductor package for management of multi-assay data

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Nextflow basic tutorial for newbie users

Big Compute Learning Labs

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...

VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

Graph-linked unified embedding for single-cell multi-omics data integration

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Improve the quality of a denovo assembly by scaffolding and gap filling

A fast, scalable, and accurate local ancestry method.

Identify phage regions in bacterial genomes for masking purposes

Tools for analyzing 10X Genomics data

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

WebAssembly modules for genomics

Grammar of Scalable Linked Interactive Nucleotide Graphics

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

R API and htmlwidget for Vitessce

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

Command line utility for manipulating Illumina-generated FastQ files.

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

Python-based UCSC genome browser snapshot-taker and gallery-maker

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Predict AMPs in (meta)genomes and peptides

A library for manipulating bioinformatics sequencing formats in Apache Spark

Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

Multilocus sequence typing by blast using the schemes from PubMLST

Forward-time simulation in Python using fwdpp

Explore rearrangements and copy-number amplifications in a cancer genome

Resource of human chromosome schematics & images

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

phenol: Phenotype ontology library

Explore gnomAD datasets on the web

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

Interactive assembly and analysis of RAD-seq data sets