Alternatives and similar repositories for STAGES

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

• interactivereport / xOmicsShiny
  xOmicsShiny: an R Shiny application for cross-omics data analysis and pathway mapping, Bioinformatics Advances, Volume 5, Issue 1, 2025, …
  ☆31Updated last week
• MaayanLab / maayanlab-bioinformatics
  A collection of useful functions for bioinformatics data analysis
  ☆24Updated 3 weeks ago
• saezlab / cosmosR
  COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data…
  ☆62Updated 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
  ☆33Updated 3 years ago
• uc-bd2k / GREIN
  GREIN : GEO RNA-seq Experiments Interactive Navigator
  ☆50Updated 6 years ago
• mdozmorov / RNA-seq_notes
  A continually expanding collection of RNA-seq tools
  ☆51Updated 9 months ago
• umccr / neoantigens
  🏺 Exploring novel tumor epitope identification
  ☆34Updated 4 years ago
• inutano / chip-atlas
  ChIP-Atlas: Browse and analyze all public ChIP/DNase-seq data on your browser
  ☆76Updated 3 weeks ago
• uio-bmi / compairr
  Comparison of Adaptive Immune Receptor Repertoires
  ☆27Updated 6 months ago
• abodein / timeOmics
  Time-Course Multi-Omics data integration
  ☆25Updated last year
• dzhakparov / GeneSelectR
  ☆19Updated last year
• gexijin / idepGolem
  ☆41Updated 2 weeks ago
• JSB-UCLA / Clipper
  A p-value-free method for controlling false discovery rates in high-throughput biological data with two conditions
  ☆39Updated 3 years ago
• IEDB / TCRMatch
  ☆29Updated last month
• s-andrews / sradownloader
  A script to make downloading of SRA/GEO data easier
  ☆31Updated last year
• frattalab / splicing
  Snakemake pipeline for running MAJIQ
  ☆23Updated last year
• IxI-97 / BiomiX
  R tool to analyse and integrate multiple -omics data
  ☆13Updated 2 months ago
• kenichi-shimada / shinyDepMap
  A shiny-based web tool for interactive analysis of DepMap data
  ☆23Updated 4 years ago
• daisybio / NEASE
  A network-based approach for exon set enrichment
  ☆15Updated 3 weeks ago
• 123xiaochen / VCFshiny
  ☆29Updated 9 months ago
• liguowang / cpgtools
  Python package to analyze DNA methylation data
  ☆43Updated 8 months ago
• complextissue / pytximport
  Feature-rich Python implementation of the tximport package for gene count estimation.
  ☆37Updated 2 weeks ago
• andreasmock / MetaboDiff
  ☆31Updated 4 years ago
• jfjlaros / demultiplex
  Versatile FASTA/FASTQ demultiplexer.
  ☆33Updated last year
• datapplab / pathview
  pathway based data integration and visualization
  ☆41Updated 4 months ago
• KirstLab / asc_seurat
  ☆24Updated last year
• alexfields / ORF-RATER
  Regression-based annotation of protein-coding sequences from ribosome profiling data
  ☆32Updated 5 years ago
• sib-swiss / RNAseq-introduction-training
  Webpage of the "Introduction to RNA-Seq: From quality control to pathway analysis - streamed" SIB course.
  ☆15Updated 10 months ago
• kuijjerlab / retriever
  Generate Robust Disease-Specific Response Signatures from the LINCS-L1000 Data
  ☆15Updated 3 years ago