Alternatives and similar repositories for STAGES

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

• saezlab / cosmosR
  COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data…
  ☆61Updated last week
• interactivereport / xOmicsShiny
  xOmicsShiny: an R Shiny application for cross-omics data analysis and pathway mapping, Bioinformatics Advances, Volume 5, Issue 1, 2025, …
  ☆31Updated last month
• nf-core / scflow
  Please consider using/contributing to https://github.com/nf-core/scdownstream
  ☆25Updated last year
• aertslab / GENIE3
  GENIE3 (GEne Network Inference with Ensemble of trees) R-package
  ☆32Updated 3 years ago
• gexijin / idepGolem
  ☆40Updated last week
• uc-bd2k / GREIN
  GREIN : GEO RNA-seq Experiments Interactive Navigator
  ☆50Updated 6 years ago
• LieberInstitute / recount3
  Explore and download data from the recount3 project
  ☆36Updated 2 months ago
• Teichlab / cell2tcr
  Inference of TCR motifs
  ☆32Updated last month
• MaayanLab / maayanlab-bioinformatics
  A collection of useful functions for bioinformatics data analysis
  ☆24Updated last month
• hart-lab / bagel
  BAGEL software
  ☆28Updated last year
• XSLiuLab / Seq2Neo
  Seq2Neo: a comprehensive pipeline for cancer neoantigen immunogenicity prediction
  ☆21Updated 2 years ago
• friedue / course_RNA-seq2019
  ☆35Updated 3 years ago
• ylab-hi / ScanNeo
  A pipeline for identifying indel derived neoantigens using RNA-Seq data
  ☆30Updated 2 years ago
• ed-lau / jcast
  Junction centric alternative splicing translator
  ☆19Updated 2 years ago
• umccr / neoantigens
  🏺 Exploring novel tumor epitope identification
  ☆34Updated 4 years ago
• cellatlas / human
  ☆44Updated 8 months ago
• LukszaLab / NeoantigenEditing
  ☆16Updated 3 years ago
• gencorefacility / r-notebooks
  Gene Set Enrichment Analysis and Over Representation Analysis analysis using R
  ☆20Updated 6 years ago
• uio-bmi / compairr
  Comparison of Adaptive Immune Receptor Repertoires
  ☆27Updated 5 months ago
• mdozmorov / RNA-seq_notes
  A continually expanding collection of RNA-seq tools
  ☆51Updated 9 months ago
• IEDB / TCRMatch
  ☆29Updated 3 weeks ago
• nf-core / mhcquant
  Identify and quantify MHC eluted peptides from mass spectrometry raw data
  ☆36Updated last week
• ktrns / scrnaseq
  Workflow for single-cell RNA-seq analysis using Seurat
  ☆42Updated last year
• tianshilu / QBRC-Neoantigen-Pipeline
  QBRC Neoantigen calling pipeline with CSiN calculation embedded
  ☆24Updated 3 years ago
• dakwok / SSNIP
  The Spatial Splicing-derived Neoantigen Identifier Pipeline (SSNIP) allows for the precise characterization of neoantigens derived from c…
  ☆18Updated 3 months ago
• frattalab / splicing
  Snakemake pipeline for running MAJIQ
  ☆23Updated last year
• bartongroup / Proteus
  R package for analysing proteomics data
  ☆49Updated 2 years ago
• dzhakparov / GeneSelectR
  ☆19Updated last year
• abodein / timeOmics
  Time-Course Multi-Omics data integration
  ☆25Updated last year
• s-andrews / sradownloader
  A script to make downloading of SRA/GEO data easier
  ☆31Updated last year