Alternatives and similar repositories for STAR-SEQR

Users that are interested in STAR-SEQR are comparing it to the libraries listed below

• 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…
  ☆45Updated 2 years ago
• sigven / gvanno
  Generic human DNA variant annotation pipeline
  ☆58Updated last year
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆31Updated 6 years ago
• vpc-ccg / svict
  Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA
  ☆29Updated last year
• pughlab / VisCap
  VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number va…
  ☆23Updated 5 years ago
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 7 years ago
• ChrisMaherLab / INTEGRATE-Vis
  ☆15Updated 2 years ago
• jeremymcrae / clinical-filter
  filtering trio-based genetic variants in VCFs for clinical review
  ☆21Updated 4 years ago
• pughlab / bamgineer
  Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
  ☆38Updated 4 years ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆48Updated this week
• viq854 / lichee
  Multi-sample cancer phylogeny reconstruction
  ☆35Updated 7 years ago
• fusiontranscripts / FusionBenchmarking
  Toolkit for benchmarking fusion transcript predictions
  ☆19Updated 11 months ago
• Oshlack / Clinker
  Gene Fusion Visualiser
  ☆51Updated 2 years ago
• eyzhao / hrdetect-pipeline
  ☆36Updated 5 years ago
• QingliGuo / FFPEsig
  Codes and Data for FFPEsig manuscript
  ☆17Updated last year
• pdxgx / neoepiscope
  predicts neoepitopes from phased somatic mutations detected using tumor/normal DNA-seq data
  ☆27Updated last year
• rgcgithub / clamms
  CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.
  ☆29Updated 4 years ago
• AmpliconSuite / CoRAL
  Reconstruction of focal amplifications with long reads
  ☆21Updated 3 weeks ago
• nf-core / circdna
  Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from…
  ☆31Updated last month
• gagneurlab / absplice
  ☆39Updated 2 weeks ago
• TomSkelly / MatchAnnot
  Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.
  ☆23Updated 9 years ago
• ccgd-profile / BreaKmer
  A method to identify structural variation from sequencing data in target regions
  ☆32Updated 4 years ago
• RahmanTeam / CAVA
  CAVA (Clinical Annotation of VAriants)
  ☆14Updated 6 years ago
• VanLoo-lab / gritic
  A tool for timing complex copy number gains in cancer.
  ☆17Updated this week
• murphycj / AGFusion
  Python package to annotate and visualize gene fusions.
  ☆63Updated 9 months ago
• pachterlab / kma
  Keep Me Around: Intron Retention Detection
  ☆29Updated 6 years ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• jrflab / modules
  MSKCC Reis-Filho Lab pipeline thingy
  ☆17Updated 2 months ago
• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 3 years ago
• rhshah / iCallSV
  A Framework to call Structural Variants from NGS based datasets
  ☆22Updated 7 years ago