Alternatives and similar repositories for chromhmm-tools

Users that are interested in chromhmm-tools are comparing it to the libraries listed below

• GreenleafLab / NucleoATACR
  R package for reading in & working with NucleoATAC outputs
  ☆26Updated 6 years ago
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆30Updated 3 years ago
• caleblareau / bap
  Bead-based single-cell atac processing
  ☆33Updated 3 years ago
• jokergoo / rGREAT
  GREAT Analysis - Functional Enrichment on Genomic Regions
  ☆87Updated 4 months ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆71Updated last year
• huishenlab / compartmap
  Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq
  ☆14Updated last month
• pachterlab / scRNA-Seq-TCC-prep
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Updated 6 years ago
• NKI-GCF / XenofilteR
  Filtering of PDX samples for mouse derived reads
  ☆28Updated 2 years ago
• JEFworks / liger
  Lightweight Iterative Gene set Enrichment in R
  ☆57Updated 9 months ago
• ParkerLab / atactk
  A toolkit for working with ATAC-seq data.
  ☆24Updated last year
• yuchaojiang / Canopy
  Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.
  ☆69Updated 3 years ago
• yuchaojiang / SCALE
  Allele-Specific Expression by Single-Cell RNA Sequencing
  ☆28Updated 4 years ago
• YosefLab / ImpulseDE2
  ☆38Updated 2 years ago
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated last year
• genesofeve / projectR
  ☆62Updated 4 months ago
• Neurosurgery-Brain-Tumor-Center-DiazLab / scell
  Single-CELL rna-seq analysis software
  ☆39Updated 7 years ago
• HumanCellAtlas / skylab
  Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
  ☆48Updated 4 months ago
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆29Updated 3 months ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆62Updated 4 years ago
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆54Updated 4 years ago
• rcavalcante / annotatr
  Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post…
  ☆27Updated 2 weeks ago
• Simon-Coetzee / motifBreakR
  A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
  ☆29Updated 11 months ago
• natsuhiko / rasqual
  Robust Allele Specific Quantification and quality controL
  ☆40Updated 3 years ago
• pachterlab / sircel
  Identify cell barcodes from single-cell genomics sequencing experiments
  ☆43Updated 3 years ago
• gagneurlab / OUTRIDER
  OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
  ☆53Updated this week
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆45Updated last year
• vivekbhr / Subread_to_DEXSeq
  Scripts to import your FeatureCounts output into DEXSeq
  ☆33Updated 6 years ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆42Updated 4 years ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆52Updated 4 years ago