Alternatives and similar repositories for ATAC-seq:

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

• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆108Updated 2 years ago
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆209Updated 2 months ago
• JiekaiLab / scTE
  ☆105Updated 11 months ago
• QuKunLab / ATAC-pipe
  Analysis pipeline for ATAC-seq Data
  ☆60Updated 3 years ago
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆157Updated 5 months 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
• hbctraining / Investigating-chromatin-biology-ChIPseq
  ☆88Updated last month
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆199Updated 3 weeks ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆94Updated 3 years ago
• TrinityCTAT / Trinity_CTAT
  ☆117Updated last year
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆189Updated last year
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated last year
• CebolaLab / ATAC-seq
  Analysis pipeline for ATAC-seq data
  ☆52Updated last year
• virajbdeshpande / AmpliconArchitect
  AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and …
  ☆144Updated 9 months ago
• ENCODE-DCC / rna-seq-pipeline
  ☆147Updated 2 years ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆178Updated 2 weeks ago
• reskejak / ATAC-seq
  Basic workflow for ATAC-seq analysis
  ☆76Updated last year
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆171Updated 8 months ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• yupenghe / methylpy
  WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
  ☆140Updated last year
• crazyhottommy / pyflow-ChIPseq
  a snakemake pipeline to process ChIP-seq files from GEO or in-house
  ☆107Updated 4 years 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 …
  ☆90Updated 2 weeks ago
• RabadanLab / arcasHLA
  Fast and accurate in silico inference of HLA genotypes from RNA-seq
  ☆126Updated 7 months ago
• kundajelab / chipseq_pipeline
  AQUAS TF and histone ChIP-seq pipeline
  ☆108Updated 2 years ago
• sztup / scarHRD
  ☆113Updated last year
• nloyfer / wgbs_tools
  tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
  ☆147Updated 3 weeks ago
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆212Updated 10 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆295Updated 3 years ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆91Updated 2 years ago