Alternatives and similar repositories for Canopy

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

• taylor-lab / hotspots
  Identifying recurrent mutations in cancer
  ☆39Updated 4 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• reiterlab / treeomics
  Decrypting somatic mutation patterns to reveal the evolution of cancer
  ☆56Updated 4 years ago
• KarchinLab / 2020plus
  Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests
  ☆50Updated last year
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆34Updated 6 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• kdkorthauer / dmrseq
  R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
  ☆62Updated 7 months ago
• PhanstielLab / Sushi
  Tools for visualizing genomics data
  ☆69Updated 4 years ago
• HumanCellAtlas / skylab
  Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
  ☆48Updated 9 months ago
• hbc / bcbioRNASeq
  R package for bcbio RNA-seq analysis.
  ☆63Updated last year
• AstraZeneca-NGS / disambiguate
  Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem
  ☆31Updated 7 years ago
• BIMSBbioinfo / genomation
  R package for genomic feature analysis and visualization
  ☆79Updated 8 months ago
• FunGeST / Palimpsest
  An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
  ☆72Updated last year
• rajanil / msCentipede
  A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
  ☆26Updated 9 years ago
• JEFworks / liger
  Lightweight Iterative Gene set Enrichment in R
  ☆57Updated last year
• 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
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆37Updated 3 years ago
• mani2012 / BatchQC
  Provides Quality Control of sequencing samples by deducing if there is batch effect and adjusts for it.
  ☆35Updated 2 years ago
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆32Updated 3 years ago
• caravagnalab / revolver
  Tumour stratification by maximum-likelihood repeated evolution from multi-region sequencing data
  ☆66Updated 3 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…
  ☆44Updated 3 years ago
• Simon-Coetzee / motifBreakR
  A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
  ☆31Updated last year
• Danko-Lab / tutorials
  Tutorials covering various topics in genomic data analysis.
  ☆16Updated 7 years ago
• gtrichard / deepStats
  deepStats: a stastitical toolbox for deeptools and genomic signals
  ☆35Updated 4 years ago
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆122Updated 2 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
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆53Updated 5 years ago
• ParkerLab / atactk
  A toolkit for working with ATAC-seq data.
  ☆24Updated last year
• jokergoo / rGREAT
  GREAT Analysis - Functional Enrichment on Genomic Regions
  ☆95Updated 2 weeks ago
• cfce / chilin
  ChIP-seq DC and QC Pipeline
  ☆36Updated 4 years ago