Alternatives and similar repositories for mgatk

Users that are interested in mgatk are comparing it to the libraries listed below

• KChen-lab / Monopogen
  SNV calling from single cell sequencing
  ☆105Updated 9 months ago
• reskejak / ATAC-seq
  Basic workflow for ATAC-seq analysis
  ☆82Updated last year
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆99Updated 9 months ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆74Updated 2 years ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆79Updated 3 years ago
• TrinityCTAT / Trinity_CTAT
  ☆117Updated last year
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆71Updated 7 months ago
• timoast / sinto
  Tools for single-cell data processing
  ☆126Updated last year
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆58Updated 3 months ago
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆69Updated 4 years ago
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆76Updated 5 months ago
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆37Updated 2 years ago
• akdess / CaSpER
  ☆86Updated 4 years ago
• snakemake-workflows / single-cell-rna-seq
  A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
  ☆103Updated 2 years ago
• QuKunLab / ATAC-pipe
  Analysis pipeline for ATAC-seq Data
  ☆61Updated 3 years ago
• single-cell-genetics / cellsnp-lite
  Efficient genotyping bi-allelic SNPs on single cells
  ☆146Updated last year
• broadinstitute / PhylogicNDT
  ☆75Updated 4 months ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated 2 years ago
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆45Updated 5 years ago
• sandberg-lab / Smart-seq3
  Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).
  ☆54Updated 3 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆95Updated 4 years ago
• AmpliconSuite / AmpliconSuite-pipeline
  A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …
  ☆68Updated last month
• LuyiTian / FLAMES
  Full-length transcriptome splicing and mutation analysis
  ☆84Updated last year
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆70Updated 9 months ago
• stjude / ROSE
  ROSE: RANK ORDERING OF SUPER-ENHANCERS
  ☆51Updated last year
• 3UTR / DaPars2
  Dynamics analysis of Alternative PolyAdenylation from RNA-seq
  ☆61Updated last year
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆110Updated 2 years ago
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆111Updated 9 months ago
• VCCRI / Sierra
  Discover differential transcript usage from polyA-captured single cell RNA-seq data
  ☆51Updated 2 years ago
• tavareshugo / tutorial_DESeq2_contrasts
  ☆63Updated last year