Alternatives and similar repositories for pVACtools

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

• MathOnco / NeoPredPipe
  Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
  ☆114Updated last year
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆208Updated last year
• RabadanLab / arcasHLA
  Fast and accurate in silico inference of HLA genotypes from RNA-seq
  ☆153Updated last year
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆107Updated this week
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆165Updated 2 weeks ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆201Updated this week
• oncokb / oncokb-annotator
  Annotates variants in MAF with OncoKB annotation.
  ☆140Updated last month
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆158Updated last month
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆138Updated 5 years ago
• ENCODE-DCC / rna-seq-pipeline
  ☆156Updated 3 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆113Updated last year
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 4 months ago
• aryeelab / guideseq
  Analysis pipeline for the GUIDE-seq assay.
  ☆81Updated 2 years ago
• broadinstitute / ichorCNA
  Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
  ☆198Updated last year
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆131Updated 3 years ago
• getzlab / rnaseqc
  Fast, efficient RNA-Seq metrics for quality control and process optimization
  ☆176Updated last year
• gagneurlab / drop
  Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
  ☆161Updated last month
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆203Updated last month
• xjtu-omics / msisensor-pro
  Microsatellite Instability (MSI) detection using high-throughput sequencing data.
  ☆115Updated 10 months ago
• kundajelab / chipseq_pipeline
  AQUAS TF and histone ChIP-seq pipeline
  ☆112Updated 3 years ago
• humanlongevity / HLA
  xHLA: Fast and accurate HLA typing from short read sequence data
  ☆113Updated 2 years ago
• kircherlab / CADD-scripts
  CADD scripts release for offline scoring. For more information about CADD, please visit our website
  ☆90Updated 3 months ago
• virajbdeshpande / AmpliconArchitect
  AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and …
  ☆157Updated last year
• Xinglab / rmats2sashimiplot
  ☆158Updated 8 months ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆175Updated last year
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆120Updated 3 years ago
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆98Updated last month
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆250Updated this week
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆128Updated 3 years ago
• VanLoo-lab / ascat
  ASCAT R package
  ☆197Updated 4 months ago