Alternatives and similar repositories for ATAC-seq

Users that are interested in ATAC-seq are comparing it to the libraries listed below

• CebolaLab / ATAC-seq
  Analysis pipeline for ATAC-seq data
  ☆76Updated last year
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆108Updated 7 months ago
• JiekaiLab / scTE
  ☆110Updated last year
• KChen-lab / Monopogen
  SNV calling from single cell sequencing
  ☆106Updated 10 months ago
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆70Updated 4 years ago
• bioinfo-ibms-pumc / SCSA
  SCSA: cell type annotation for single-cell RNA-seq data
  ☆91Updated 2 years ago
• 3UTR / DaPars2
  Dynamics analysis of Alternative PolyAdenylation from RNA-seq
  ☆61Updated 2 years ago
• QuKunLab / ATAC-pipe
  Analysis pipeline for ATAC-seq Data
  ☆62Updated 4 years ago
• fl-yu / CUT-RUNTools-2.0
  CUT&RUN and CUT&Tag data processing and analysis
  ☆111Updated 6 months ago
• nf-core / cutandrun
  Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream …
  ☆99Updated 3 weeks ago
• cellgeni / STARsolo
  wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
  ☆64Updated 3 months ago
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆39Updated last week
• single-cell-genetics / cellsnp-lite
  Efficient genotyping bi-allelic SNPs on single cells
  ☆150Updated last year
• MGI-tech-bioinformatics / DNBelab_C_Series_HT_scRNA-analysis-software
  An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets
  ☆111Updated 2 weeks ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆74Updated 2 years ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆112Updated 2 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
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆97Updated 2 years ago
• rpolicastro / scProportionTest
  ☆71Updated 2 years ago
• scottzijiezhang / m6A-seq_analysis_workflow
  A pipeline to process m6A-seq data and down stream analysis.
  ☆45Updated 5 years ago
• TrinityCTAT / Trinity_CTAT
  ☆118Updated 2 years ago
• akdess / CaSpER
  ☆88Updated 4 years ago
• sjdlabgroup / SAHMI
  ☆84Updated last year
• hamidghaedi / Enrichment-Analysis
  From RNA-seq raw reads to enriched pathways by DEGs
  ☆32Updated last year
• xryanglab / RiboCode
  release version
  ☆54Updated 3 years ago
• TheHumphreysLab / plot1cell
  ☆115Updated 2 weeks ago
• timoast / sinto
  Tools for single-cell data processing
  ☆126Updated last year
• epi2me-labs / wf-single-cell
  ☆95Updated last month
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆80Updated 3 years ago
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆69Updated 10 months ago