Alternatives and similar repositories for ATAC-pipe

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

• GreenleafLab / 10x-scATAC-2019
  Publication Page for Satpathy*, Granja* et al 2019
  ☆95Updated 5 years ago
• reskejak / ATAC-seq
  Basic workflow for ATAC-seq analysis
  ☆82Updated last year
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆68Updated 3 years ago
• stjude / ROSE
  ROSE: RANK ORDERING OF SUPER-ENHANCERS
  ☆50Updated last year
• crazyhottommy / pyflow-ATACseq
  ATAC-seq snakemake pipeline
  ☆89Updated 5 years ago
• 3UTR / DaPars2
  Dynamics analysis of Alternative PolyAdenylation from RNA-seq
  ☆61Updated last year
• scottzijiezhang / m6A-seq_analysis_workflow
  A pipeline to process m6A-seq data and down stream analysis.
  ☆45Updated 5 years ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆79Updated 3 years ago
• tallulandrews / scRNASeqPipeline
  ☆118Updated 6 years ago
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆108Updated 6 months ago
• cxzhu / Paired-Tag
  Analysis of Paired-Tag datasets
  ☆42Updated last year
• KChen-lab / Monopogen
  SNV calling from single cell sequencing
  ☆104Updated 8 months ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆74Updated 2 years ago
• 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
  ☆103Updated this week
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆70Updated 8 months ago
• JiekaiLab / scTE
  ☆108Updated last year
• bioinfo-ibms-pumc / SCSA
  SCSA: cell type annotation for single-cell RNA-seq data
  ☆91Updated 2 years ago
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆69Updated 5 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆58Updated 2 months ago
• TrinityCTAT / Trinity_CTAT
  ☆117Updated last year
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆99Updated 8 months ago
• AmpliconSuite / AmpliconSuite-pipeline
  A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …
  ☆68Updated last month
• fl-yu / CUT-RUNTools-2.0
  CUT&RUN and CUT&Tag data processing and analysis
  ☆110Updated 5 months ago
• cellgeni / STARsolo
  wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
  ☆61Updated 2 months ago
• xryanglab / RiboCode
  release version
  ☆54Updated 3 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
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆95Updated 4 years ago
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆76Updated 5 months ago
• akdess / CaSpER
  ☆86Updated 4 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆59Updated 4 years ago