Alternatives and similar repositories for facets:

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

• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆104Updated last year
• VanLoo-lab / ascat
  ASCAT R package
  ☆180Updated last month
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆141Updated 2 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆132Updated 10 months ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 6 months ago
• raerose01 / deconstructSigs
  deconstructSigs
  ☆141Updated 2 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆158Updated 2 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆145Updated 2 years ago
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• 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…
  ☆52Updated 4 years ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• broadinstitute / PhylogicNDT
  ☆72Updated 3 weeks ago
• sztup / scarHRD
  ☆115Updated last year
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆97Updated 7 months ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆134Updated 2 weeks ago
• hdng / clonevol
  Inferring and visualizing clonal evolution in multi-sample cancer sequencing
  ☆147Updated 4 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 5 months ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆190Updated 2 years ago
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆94Updated 4 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 5 years ago
• UMCUGenetics / MutationalPatterns
  R package for extracting and visualizing mutational patterns in base substitution catalogues
  ☆106Updated 2 years ago
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆159Updated 6 months ago
• oncokb / oncokb-annotator
  Annotates variants in MAF with OncoKB annotation.
  ☆130Updated this week
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 4 years ago
• virajbdeshpande / AmpliconArchitect
  AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and …
  ☆146Updated 10 months ago
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆199Updated last year
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆214Updated 11 months ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆109Updated 2 years ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆123Updated 2 years ago