Alternatives and similar repositories for facets

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

• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆137Updated last year
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆100Updated 4 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆113Updated last year
• raerose01 / deconstructSigs
  deconstructSigs
  ☆144Updated 2 years ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆141Updated 5 months ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆197Updated 4 months ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆89Updated 8 years ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆142Updated 3 years ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆105Updated 4 years ago
• hdng / clonevol
  Inferring and visualizing clonal evolution in multi-sample cancer sequencing
  ☆149Updated 5 years ago
• sztup / scarHRD
  ☆119Updated 2 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 4 months ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆98Updated last year
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆159Updated 6 months ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 5 years ago
• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆55Updated 5 years ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆128Updated 3 years ago
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆136Updated last year
• guigolab / ggsashimi
  Command-line tool for the visualization of splicing events across multiple samples
  ☆136Updated last year
• ding-lab / msisensor
  microsatellite instability detection using tumor only or paired tumor-normal data
  ☆132Updated 5 years ago
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆229Updated last year
• chrisamiller / fishplot
  Create timecourse "fish plots" that show changes in the clonal architecture of tumors
  ☆171Updated last week
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆118Updated 7 years ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆123Updated 2 months ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆138Updated 5 years ago
• genome / sciclone
  An R package for inferring the subclonal architecture of tumors
  ☆121Updated 2 years ago
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆78Updated 5 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆96Updated 4 years ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆231Updated 8 months ago