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
  ☆106Updated 4 years ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆74Updated 2 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆99Updated 8 months ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆110Updated 2 years ago
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆68Updated 3 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆95Updated 4 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆70Updated 6 months ago
• TrinityCTAT / Trinity_CTAT
  ☆117Updated last year
• crazyhottommy / pyflow-ATACseq
  ATAC-seq snakemake pipeline
  ☆89Updated 5 years ago
• ZhengXia / dapars
  DaPars(Dynamic analysis of Alternative PolyAdenylation from RNA-seq)
  ☆51Updated 2 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆58Updated 2 months 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…
  ☆59Updated 5 years ago
• Henikoff / Cut-and-Run
  ☆30Updated 7 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆81Updated 6 months ago
• GoekeLab / proActiv
  Estimation of Promoter Activity from RNA-Seq data
  ☆53Updated 3 weeks ago
• FenyoLab / L1EM
  Estimate locus specific human LINE-1 expression.
  ☆36Updated 2 years ago
• indrops / indrops
  Pipeline for processing inDrops sequencing data
  ☆76Updated 6 years ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago
• AAlhendi1707 / countToFPKM
  Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)
  ☆62Updated 4 years ago
• crazyhottommy / pyflow-ChIPseq
  a snakemake pipeline to process ChIP-seq files from GEO or in-house
  ☆109Updated 5 years ago
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆110Updated 8 months ago
• 3UTR / DaPars2
  Dynamics analysis of Alternative PolyAdenylation from RNA-seq
  ☆61Updated last year
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆108Updated 6 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.
  ☆103Updated 2 years ago
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆122Updated last year
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆116Updated 6 months ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆114Updated 3 years ago
• vanheeringen-lab / gimmemotifs
  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…
  ☆120Updated last year
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆43Updated 7 years ago
• vaquerizaslab / fanc
  FAN-C: Framework for the ANalysis of C-like data
  ☆116Updated last year