Alternatives and similar repositories for ChromHMM:

Users that are interested in ChromHMM are comparing it to the libraries listed below

• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆67Updated last month
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆106Updated 4 years ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated last year
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• AmpliconSuite / AmpliconSuite-pipeline
  A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …
  ☆62Updated this week
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 3 months ago
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆60Updated 3 years ago
• kundajelab / phantompeakqualtools
  This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…
  ☆56Updated 4 years ago
• broadinstitute / PhylogicNDT
  ☆71Updated 9 months ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆93Updated 3 years ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆111Updated 2 years ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆122Updated 4 years ago
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆119Updated 6 years ago
• reskejak / ATAC-seq
  Basic workflow for ATAC-seq analysis
  ☆73Updated 11 months ago
• QuKunLab / ATAC-pipe
  Analysis pipeline for ATAC-seq Data
  ☆60Updated 3 years ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆107Updated 2 years ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆165Updated 7 months ago
• GreenleafLab / 10x-scATAC-2019
  Publication Page for Satpathy*, Granja* et al 2019
  ☆92Updated 4 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆54Updated this week
• AAlhendi1707 / countToFPKM
  Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)
  ☆62Updated 3 years ago
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆32Updated 2 years ago
• crazyhottommy / pyflow-ATACseq
  ATAC-seq snakemake pipeline
  ☆86Updated 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.
  ☆101Updated 2 years ago
• KChen-lab / Monopogen
  SNV calling from single cell sequencing
  ☆93Updated 3 months ago
• OlgaVT / Alternative-Splicing-Tools
  A list of alternative splicing analysis resources
  ☆41Updated 3 months ago
• sztup / scarHRD
  ☆109Updated last year
• cancer-genomics / delfi_scripts
  ☆72Updated 3 years ago
• gatk-workflows / gatk4-rnaseq-germline-snps-indels
  Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
  ☆73Updated 3 years ago
• sandberg-lab / Smart-seq3
  Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).
  ☆51Updated 3 years ago