Alternatives and similar repositories for PACT

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

• vanallenlab / retained-intron-neoantigen-pipeline
  Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.
  ☆28Updated 4 years ago
• jiujiezz / tsnad
  Detecting somatic mutations and predicting tumor-specific neo-antigens
  ☆28Updated 3 years ago
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated last year
• khuranalab / CompositeDriver
  Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers
  ☆15Updated 6 years ago
• morrislab / pairtree
  Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneit…
  ☆37Updated last year
• Oshlack / Slinker
  Slinker offers a succinct and complementary method to visualise RNA-Seq data through superTranscripts.
  ☆19Updated 2 years ago
• sigven / oncoEnrichR
  Explore the cancer relevance of your gene list
  ☆51Updated 2 months ago
• aertslab / PUMATAC
  Pipeline for Universal Mapping of ATAC-seq
  ☆25Updated last year
• mskilab-org / nf-jabba
  ☆13Updated this week
• qqwang-berkeley / JUM
  A tool for annotation-free differential analysis of tissue-specific pre-mRNA alternative splicing patterns
  ☆28Updated 2 years ago
• cboix / epimap_vis
  Code for EpiMap data browser
  ☆14Updated 11 months ago
• huyustats / SCATS
  A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
  ☆22Updated last year
• fusiontranscripts / FusionBenchmarking
  Toolkit for benchmarking fusion transcript predictions
  ☆19Updated 8 months ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆30Updated last year
• icbi-lab / NeoFuse
  NeoFuse is a user-friendly pipeline for the prediction of fusion neoantigens from tumor RNA-seq data.
  ☆19Updated 2 years ago
• lkuchenb / MultiHLA
  WES HLA Typing based on multiple alternative tools
  ☆16Updated 4 years ago
• de-Boer-Lab / MAUDE
  Mean Alterations Using Discrete Expression
  ☆14Updated last year
• zhongw2 / GeneTEFlow
  ☆23Updated 3 years ago
• oicr-gsi / sequenza
  Workflow for Sequenza, cellularity and ploidy
  ☆18Updated last month
• TRON-Bioinformatics / splice2neo
  R package to analyze aberrant splicing junctions in tumor samples to identify neoepitopes
  ☆14Updated last month
• parklab / MSIprofiler
  Repo that aids in the detection of microsatellite instabilities (MSI) from sequencing data
  ☆20Updated last year
• openvax / isovar
  Assembly of RNA reads to determine the effect of a cancer mutation on protein sequence
  ☆25Updated 7 months ago
• lagelab / quack
  Machine learning algorithm to predict biological pathway relationships based on functional genomics networks
  ☆20Updated 6 years ago
• jsalignon / cactus
  Chromatin ACcessibility and Transcriptomics Unifying Software
  ☆16Updated 6 months ago
• ashleymaeconard / TIMEOR
  TIMEOR: Trajectory Inference and Mechanism Exploration with Omics Data in R
  ☆16Updated 3 years ago
• broadinstitute / mix_seq_ms
  Code associated with MIX-seq manuscript
  ☆15Updated 4 years ago
• amf71 / ECLIPSE
  ☆11Updated last year
• pdxgx / neoepiscope
  predicts neoepitopes from phased somatic mutations detected using tumor/normal DNA-seq data
  ☆27Updated last year
• caravagnalab / CNAqc
  CNAqc - Copy Number Alteration (CNA) Quality Check package
  ☆21Updated last week
• yigbt / multiGSEA
  The `multiGSEA` R package was designed to run a robust GSEA-based pathway enrichment for multiple omics layers.
  ☆18Updated 3 weeks ago