Alternatives and similar repositories for ChromHMM

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

• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆109Updated 4 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆72Updated 10 months ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated 2 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆99Updated last year
• TrinityCTAT / Trinity_CTAT
  ☆120Updated 2 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆61Updated 2 months ago
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆73Updated 4 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆83Updated 10 months ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆118Updated 2 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…
  ☆60Updated 5 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
  ☆60Updated 4 years ago
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆118Updated 7 years ago
• AmpliconSuite / AmpliconSuite-pipeline
  A quickstart tool for AmpliconArchitect. Enables all steps (alignment, CNV calling, seed interval detection) prior to running AmpliconArc…
  ☆75Updated this week
• GoekeLab / proActiv
  Estimation of Promoter Activity from RNA-Seq data
  ☆56Updated 4 months ago
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆39Updated 3 weeks ago
• vanheeringen-lab / gimmemotifs
  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…
  ☆122Updated 2 months ago
• ZhengXia / dapars
  DaPars(Dynamic analysis of Alternative PolyAdenylation from RNA-seq)
  ☆52Updated 3 years ago
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆109Updated 10 months ago
• QuKunLab / ATAC-pipe
  Analysis pipeline for ATAC-seq Data
  ☆62Updated 4 years ago
• Henikoff / Cut-and-Run
  ☆32Updated 7 years ago
• indrops / indrops
  Pipeline for processing inDrops sequencing data
  ☆76Updated 7 years ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆120Updated this week
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆112Updated last month
• crazyhottommy / pyflow-ATACseq
  ATAC-seq snakemake pipeline
  ☆88Updated 5 years ago
• xryanglab / xtail
  Genome-wide assessment of differential translations with ribosome profiling data
  ☆20Updated 7 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.
  ☆104Updated 3 years ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆41Updated 3 years ago
• BUStools / bustools
  Tools for working with BUS files
  ☆102Updated 6 months ago
• AAlhendi1707 / countToFPKM
  Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)
  ☆63Updated 4 years ago