OpenGenomics / mc3

Related projects ⓘ

Alternatives and complementary repositories for mc3

• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆41Updated 2 years ago
• PeeperLab / CopywriteR
  DNA copy number detection from off-target sequence data
  ☆30Updated 6 years ago
• UMCUGenetics / CHORD
  An R package for predicting HR deficiency from mutation contexts
  ☆27Updated last year
• kgori / sigfit
  Flexible Bayesian inference of mutational signatures
  ☆33Updated last year
• umccr / vcf_stuff
  📊Evaluating, filtering, comparing, and visualising VCF
  ☆27Updated last year
• chrisamiller / copyCat
  a parallel R package for detecting copy-number alterations from short sequencing reads
  ☆22Updated 3 years ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆69Updated 5 months ago
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆30Updated 5 years ago
• cancerit / alleleCount
  Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…
  ☆43Updated 2 years ago
• mskcc / facets-suite
  Utility functions for FACETS
  ☆34Updated 8 months ago
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆26Updated 2 years ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆39Updated 7 years ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆49Updated 2 years ago
• FJD-CEPH / aCNViewer
  Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
  ☆28Updated 5 years ago
• AstraZeneca-NGS / disambiguate
  Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem
  ☆29Updated 6 years ago
• namphuon / ViFi
  Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
  ☆27Updated 3 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆39Updated 3 years ago
• cfce / chilin
  ChIP-seq DC and QC Pipeline
  ☆34Updated 3 years ago
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆29Updated last month
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆37Updated 2 years ago
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated 11 months ago
• eyzhao / hrdetect-pipeline
  ☆33Updated 5 years ago
• rcavalcante / annotatr
  Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post…
  ☆26Updated 3 months ago
• ding-lab / PanCanAtlasGermline
  ☆43Updated 6 years ago
• ParkerLab / atactk
  A toolkit for working with ATAC-seq data.
  ☆24Updated 5 months ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆29Updated last year
• ChrisMaherLab / ClonEvol
  ☆13Updated 7 years ago
• shbrief / CNVWorkflow_Code
  CNV analysis workflow code for the manuscript
  ☆13Updated 4 years ago
• mahmoudibrahim / JAMM
  JAMM Peak Finder for Sequencing Datasets
  ☆28Updated 4 years ago