Alternatives and similar repositories for facets:

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

• PoisonAlien / somaticfreq
  knowledge-based genotyping of cancer hotspots from the tumor BAM files
  ☆20Updated 3 years ago
• caravagnalab / CNAqc
  CNAqc - Copy Number Alteration (CNA) Quality Check package
  ☆19Updated 2 months ago
• caravagnalab / mobster
  Model-based subclonal deconvolution from bulk sequencing.
  ☆33Updated 2 weeks ago
• fsvarn / GLASSx
  GLASS consortium
  ☆13Updated 2 years ago
• luisgls / SOPRANO
  SelectiOn in PRotein ANnotated regiOns. Adapted dN/dS based method to detect selection in specific protein regions
  ☆11Updated 8 months ago
• khuranalab / CompositeDriver
  Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
  ☆15Updated 6 years ago
• theislab / hadge
  Comprehensive pipeline for donor demultiplexing in single cell
  ☆24Updated 7 months ago
• marcjwilliams1 / neutralitytestr
  Testing a neutral evolution model on cancer sequencing data
  ☆10Updated 3 years ago
• gerstung-lab / PCAWG-11
  Code accompanying "The evolutionary history of 2,658 cancers", Nature 578, 122–128 (2020)
  ☆17Updated 5 years ago
• amf71 / cloneMap
  An R package to plot maps of clone distributions in somatic evolution
  ☆17Updated last year
• hanasusak / cDriver
  cDriver R package for finding candidate driver genes in cancers
  ☆18Updated 7 years ago
• eudoraleer / scasa
  SCASA: Single cell transcript quantification tool
  ☆19Updated last year
• Papatheodorou-Group / CATD_snakemake
  Snakemake pipeline for benchmarking cell-type deconvolution methods and deconvolving real bulk RNA-seq data with the use of scRNA-seq dat…
  ☆15Updated 5 months ago
• yuchaojiang / SCALE
  Allele-Specific Expression by Single-Cell RNA Sequencing
  ☆28Updated 4 years ago
• yizhak-lab-ccg / RNA_MUTECt_WMN
  ☆22Updated 2 years ago
• ConesaLab / acorde
  Isoform co-usage networks from single-cell RNA-seq data
  ☆15Updated 10 months ago
• ebi-gene-expression-group / r-seurat-scripts
  Scripts to install as a Bioconda package for making workflows
  ☆18Updated 4 months ago
• markowetzlab / Drews2022_CIN_Compendium
  Main repository for Drews et al. (Nature, 2022)
  ☆39Updated last year
• rnabioco / scraps
  Single-cell RNA Processing Software
  ☆11Updated 3 months ago
• AlexandrovLab / SigProfilerTopography
  SigProfilerTopography allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA re…
  ☆19Updated last month
• beroukhim-lab / ascets
  This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm…
  ☆14Updated 11 months ago
• TheJacksonLaboratory / BRCA-LRseq-pipeline
  Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.
  ☆14Updated 2 years ago
• gersteinlab / siglasso
  Optimizing Cancer Mutation Signatures Jointly with Sampling Likelihood
  ☆10Updated 2 years ago
• vanallenlab / retained-intron-neoantigen-pipeline
  Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.
  ☆28Updated 3 years ago
• single-cell-genetics / singlecell_neuroseq_paper
  Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
  ☆21Updated 6 months ago
• genemine / iread
  iread
  ☆23Updated 3 years ago
• asoltis / MutEnricher
  Somatic coding and non-coding mutation enrichment analysis for tumor WGS data
  ☆10Updated 3 years ago
• PoolLab / ReferenceEnhancer
  ☆20Updated last year
• crazyhottommy / scCustomize
  Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
  ☆16Updated 3 years ago
• FJD-CEPH / aCNViewer
  Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
  ☆28Updated 5 years ago