Alternatives and similar repositories for chisel

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

• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆31Updated 9 months ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆65Updated 5 years ago
• biosinodx / SCcaller
  Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data
  ☆35Updated last year
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆41Updated 3 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• raphael-group / decifer
  DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell frac…
  ☆22Updated last year
• cbg-ethz / SCICoNE
  Single-cell copy number calling and event history reconstruction.
  ☆27Updated last year
• HorvathLab / NGS
  Next-Gen Sequencing tools from the Horvath Lab
  ☆44Updated 3 months ago
• kundajelab / idr
  IDR
  ☆31Updated 2 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆40Updated 4 years ago
• gagneurlab / OUTRIDER
  OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
  ☆54Updated 2 months ago
• nloyfer / meth_atlas
  ☆53Updated 3 years ago
• YeoLab / outrigger
  Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
  ☆67Updated 5 years ago
• natsuhiko / rasqual
  Robust Allele Specific Quantification and quality controL
  ☆40Updated 4 years ago
• ernstlab / full_stack_ChromHMM_annotations
  Data of genome annotation from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes
  ☆38Updated last year
• nskvir / RepEnrich
  RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆28Updated 3 years ago
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆32Updated 3 years ago
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆30Updated 10 months ago
• broadinstitute / RNA_MUTECT_1.0-1
  ☆38Updated 5 years ago
• shahcompbio / hmmcopy_utils
  Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.
  ☆42Updated 4 years ago
• r3fang / snATAC
  <<------ Use SnapATAC!!
  ☆26Updated 6 years ago
• parklab / MuSiCal
  A comprehensive toolkit for mutational signature analysis
  ☆42Updated last year
• aryeelab / hichipper
  A preprocessing and QC pipeline for HiChIP data
  ☆40Updated 3 years ago
• dphansti / mango
  chia pet analysis software
  ☆25Updated 6 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆61Updated 3 months ago
• parklab / ShatterSeek
  ☆72Updated 2 years ago
• kundajelab / ataqc
  ☆17Updated 6 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆72Updated last year
• vivekbhr / Subread_to_DEXSeq
  Scripts to import your FeatureCounts output into DEXSeq
  ☆34Updated 7 years ago