Alternatives and similar repositories for ATAC-pipe

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

• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆83Updated 3 years ago
• reskejak / ATAC-seq
  Basic workflow for ATAC-seq analysis
  ☆92Updated last year
• GreenleafLab / 10x-scATAC-2019
  Publication Page for Satpathy*, Granja* et al 2019
  ☆95Updated 5 years ago
• KChen-lab / Monopogen
  SNV calling from single cell sequencing
  ☆118Updated last year
• cxzhu / Paired-Tag
  Analysis of Paired-Tag datasets
  ☆43Updated 2 years ago
• JiekaiLab / scTE
  ☆114Updated last year
• TrinityCTAT / Trinity_CTAT
  ☆120Updated 2 years ago
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆77Updated 4 years ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated 2 years ago
• crazyhottommy / pyflow-ATACseq
  ATAC-seq snakemake pipeline
  ☆88Updated 5 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.
  ☆105Updated 3 years ago
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆110Updated last year
• scottzijiezhang / m6A-seq_analysis_workflow
  A pipeline to process m6A-seq data and down stream analysis.
  ☆45Updated 5 years ago
• tallulandrews / scRNASeqPipeline
  ☆118Updated 7 years ago
• stjude / ROSE
  ROSE: RANK ORDERING OF SUPER-ENHANCERS
  ☆63Updated 2 months ago
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆68Updated 6 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆61Updated 4 months ago
• 3UTR / DaPars2
  Dynamics analysis of Alternative PolyAdenylation from RNA-seq
  ☆63Updated 2 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆98Updated last year
• bioinfo-ibms-pumc / SCSA
  SCSA: cell type annotation for single-cell RNA-seq data
  ☆94Updated 2 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆73Updated last year
• akdess / CaSpER
  ☆87Updated 4 years ago
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆74Updated last year
• CebolaLab / ATAC-seq
  Analysis pipeline for ATAC-seq data
  ☆85Updated 2 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆96Updated 4 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆63Updated 5 years ago
• fl-yu / CUT-RUNTools-2.0
  CUT&RUN and CUT&Tag data processing and analysis
  ☆113Updated 11 months ago
• kharchenkolab / dropEst
  Pipeline for initial analysis of droplet-based single-cell RNA-seq data
  ☆95Updated 3 years ago
• sandberg-lab / Smart-seq3
  Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).
  ☆57Updated 4 years ago
• AmpliconSuite / AmpliconSuite-pipeline
  A quickstart tool for AmpliconArchitect. Enables all steps (alignment, CNV calling, seed interval detection) prior to running AmpliconArc…
  ☆77Updated this week