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
  ☆92Updated 4 years ago
• cxzhu / Paired-Tag
  Analysis of Paired-Tag datasets
  ☆39Updated last year
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated last year
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆68Updated 5 years ago
• stjude / ROSE
  ROSE: RANK ORDERING OF SUPER-ENHANCERS
  ☆45Updated 7 months ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆77Updated 2 years ago
• scottzijiezhang / m6A-seq_analysis_workflow
  A pipeline to process m6A-seq data and down stream analysis.
  ☆43Updated 4 years ago
• reskejak / ATAC-seq
  Basic workflow for ATAC-seq analysis
  ☆75Updated last year
• xryanglab / RiboCode
  release version
  ☆51Updated 2 years ago
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆60Updated 3 years ago
• TrinityCTAT / Trinity_CTAT
  ☆116Updated 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
  ☆84Updated 5 months ago
• 3UTR / DaPars2
  Dynamics analysis of Alternative PolyAdenylation from RNA-seq
  ☆57Updated last year
• AmpliconSuite / AmpliconSuite-pipeline
  A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …
  ☆63Updated 2 weeks ago
• JiekaiLab / scTE
  ☆105Updated 10 months ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 4 months ago
• CebolaLab / ATAC-seq
  Analysis pipeline for ATAC-seq data
  ☆48Updated last year
• KChen-lab / Monopogen
  SNV calling from single cell sequencing
  ☆93Updated 4 months ago
• akdess / CaSpER
  ☆83Updated 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.
  ☆101Updated 2 years ago
• crazyhottommy / pyflow-ATACseq
  ATAC-seq snakemake pipeline
  ☆86Updated 5 years ago
• harvardinformatics / ATAC-seq
  ☆127Updated 6 years ago
• AAlhendi1707 / countToFPKM
  Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)
  ☆62Updated 3 years ago
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆74Updated 2 weeks ago
• rpolicastro / scProportionTest
  ☆61Updated last year
• livnatje / ImmuneResistance
  This resource provides the code developed in the study of Jerby-Arnon _et al. "Single-cell RNA-seq of melanoma ecosystems reveals sources…
  ☆72Updated 6 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆67Updated 2 months ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆94Updated 3 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆57Updated 4 years ago
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆33Updated 2 years ago