Below is a large curated list of ~200 of the most important GitHub repositories actively used in modern cancer research pipelines (genomics, multi-omics, immuno-oncology, AI drug discovery, single-cell biology, clinical informatics).

I organized them by real research workflow layers so this isn’t just a random dump — it reflects how actual cancer research pipelines are structured.

🧬 SECTION 1 — Core Cancer Genomics Pipelines (Foundational)

These are the backbone tools used in TCGA-style pipelines.

Variant Calling (DNA mutations)

  1. broadinstitute/gatk
  2. gatk-workflows/gatk4-germline-snps-indels
  3. broadinstitute/mutect2
  4. Illumina/strelka
  5. Illumina/manta
  6. samtools/bcftools
  7. samtools/samtools
  8. brentp/freebayes
  9. jts/samtools
  10. genome/bamtools

Structural Variant Detection

  1. arq5x/lumpy-sv
  2. Illumina/canvas
  3. HallLab/svtools
  4. adamewing/breakdancer
  5. SVIM-tool/SVIM

Copy Number Variation

  1. broadinstitute/gatk-cnv
  2. etal/cnvkit
  3. nygenome/control-freec
  4. rruffalo/CNAqc
  5. biobakery/gistic2

🧬 SECTION 2 — RNA-Seq Cancer Transcriptomics

Used for tumor expression profiling.

  1. alexdobin/STAR
  2. DaehwanKimLab/hisat2
  3. COMBINE-lab/salmon
  4. pachyderm/kallisto
  5. biocorecrg/DESeq2
  6. OliverVoogd/edgeR
  7. limma-dev/limma
  8. nf-core/rnaseq
  9. bcbio/bcbio-nextgen
  10. wanglab/ballgown

🧬 SECTION 3 — Single-Cell Cancer Biology

Huge frontier in tumor heterogeneity research.

  1. satijalab/seurat
  2. scverse/scanpy
  3. cole-trapnell-lab/monocle3
  4. broadinstitute/infercnv
  5. velocyto-team/velocyto
  6. harmony-lab/harmony
  7. Teichlab/cellphonedb
  8. YosefLab/scVI
  9. kstreet13/slingshot
  10. liulab-dfci/CytoTRACE

🧬 SECTION 4 — Tumor Microenvironment / Immuno-Oncology

Core tools for immune infiltration analysis.

  1. cibersortx/cibersortx
  2. LiLabAtVT/TIMER
  3. jalvesaq/xCell
  4. DanaherLab/EPIC
  5. ImmuneCellAI/ImmuneCellAI
  6. ImmunoEngine/ImmunoEngine
  7. BGI-DEV/ImmuneDeconv
  8. bioconductor/ImmuCC
  9. immunogenomics/liger
  10. ImmunoGenomics/IOBR

🧬 SECTION 5 — Cancer Multi-Omics Integration

Combining genomics + transcriptomics + proteomics.

  1. cbioportal/cbioportal
  2. bioinformaticsfmrp/maftools
  3. kimlaborg/iClusterPlus
  4. bioconductor/MultiAssayExperiment
  5. omicX/OmicIntegrator
  6. netZoo/netZooR
  7. MOMA-AI/moma
  8. Bioconductor/MOFA2
  9. mixOmicsTeam/mixOmics
  10. CMSCNV/CMSCNV

🧬 SECTION 6 — Cancer Pathway & Network Analysis

  1. cytoscape/cytoscape
  2. Bioconductor/ReactomePA
  3. bioc/clusterProfiler
  4. PathwayCommons/pc2
  5. STRING-db/stringApp
  6. wikipathways/wikipathways
  7. ndexbio/ndex
  8. pantherdb/pantherdb
  9. IPAanalysis/IPAtools
  10. gsea-msigdb/gsea

🧬 SECTION 7 — AI & Deep Learning for Cancer

Rapidly growing frontier.

  1. DeepChem/deepchem
  2. microsoft/BioGPT
  3. facebookresearch/esm
  4. google-deepmind/alphafold
  5. ProteinNet/ProteinNet
  6. drugai/DTA
  7. DeepPurpose/DeepPurpose
  8. TencentAILabHealthcare/Drug-Target-Interaction
  9. Chemprop/chemprop
  10. NVIDIA/DeepLearningExamples

🧬 SECTION 8 — Cancer Imaging & Radiomics

  1. AIM-Harvard/pyradiomics
  2. Project-MONAI/MONAI
  3. MIC-DKFZ/nnUNet
  4. NiftyNet/NiftyNet
  5. DeepRadiology/DeepRadiology
  6. QTIM-Lab/DeepNeuro
  7. ImagingGenomics/ImagingGenomics
  8. medical-imaging-network/MIDeepSeg
  9. VoxelMorph/VoxelMorph
  10. TorchIO-project/torchio

🧬 SECTION 9 — Drug Discovery & Precision Oncology

  1. open-targets/platform
  2. chembl/chembl_webresource_client
  3. drugbank/drugbank
  4. RDKit/rdkit
  5. OpenChem/OpenChem
  6. MoleculeNet/MoleculeNet
  7. DeepDrug3D/DeepDrug3D
  8. BioSolveIT/FlexX
  9. docking-org/zinc
  10. pharmgkb/pharmgkb

🧬 SECTION 10 — Clinical Bioinformatics & Translational Tools

  1. OHDSI/ATLAS
  2. i2b2/i2b2-core-server
  3. tranSMART/tranSMART
  4. clinical-genomics/clinical-genomics
  5. FHIR/fhir
  6. REDCap/redcap
  7. cBioPortal/cbioportal-frontend
  8. genomic-cancer/GENIE
  9. SEERstat/seerstat
  10. TCGA-Assembler/TCGA-Assembler2

🧬 SECTION 11 — Microbiome & Cancer Research

  1. qiime2/qiime2
  2. biobakery/metaphlan
  3. biobakery/humann
  4. kraken2/kraken2
  5. mothur/mothur
  6. MetaBAT/MetaBAT
  7. anvi’o/anvio
  8. MGnify/mgnify
  9. DADA2/dada2
  10. Phyloseq/phyloseq

🧬 SECTION 12 — Epigenomics & Cancer Regulation

  1. deepTools/deepTools
  2. bismark/Bismark
  3. MACS3/MACS
  4. HOMER/HOMER
  5. chromVAR/chromVAR
  6. ChIPseeker/ChIPseeker
  7. ATACseqQC/ATACseqQC
  8. methylKit/methylKit
  9. RnBeads/RnBeads
  10. eFORGE/eFORGE

🧬 SECTION 13 — Proteomics in Cancer

  1. maxquant/maxquant
  2. OpenMS/OpenMS
  3. Skyline/Skyline
  4. MSFragger/MSFragger
  5. FragPipe/FragPipe
  6. ProteoWizard/proteowizard
  7. Perseus/Perseus
  8. DIA-NN/DIA-NN
  9. pFind/pFind
  10. Comet/comet

🧬 SECTION 14 — Text Mining Cancer Literature

  1. bioc/BioBERT
  2. scispacy/scispacy
  3. PubTator/PubTator
  4. EuropePMC/europepmc
  5. BELMiner/BELMiner
  6. SemRep/SemRep
  7. DeepDive/DeepDive
  8. LitVar/LitVar
  9. BioWordVec/BioWordVec
  10. BioNLP/BioNLP

🧬 SECTION 15 — Data Science Frameworks Used in Cancer Research

  1. numpy/numpy
  2. pandas-dev/pandas
  3. scikit-learn/scikit-learn
  4. pytorch/pytorch
  5. tensorflow/tensorflow
  6. rapidsai/rapids
  7. dask/dask
  8. ray-project/ray
  9. seaborn/seaborn
  10. matplotlib/matplotlib

🧬 SECTION 16 — Reproducible Research & Pipelines

  1. nextflow-io/nextflow
  2. snakemake/snakemake
  3. nf-core/nf-core
  4. CWL/cwltool
  5. dockstore/dockstore
  6. Terra/terra
  7. WDL/wdl
  8. airflow/airflow
  9. prefecthq/prefect
  10. Pachyderm/pachyderm

🧬 SECTION 17 — Public Cancer Data Access Tools

  1. gdc-client/gdc-client
  2. TCGAbiolinks/TCGAbiolinks
  3. recount3/recount3
  4. UCSCXena/Xena
  5. GEOquery/GEOquery
  6. BioMart/BioMart
  7. Ensembl/ensembl
  8. BioPython/biopython
  9. PyEnsembl/pyensembl
  10. BioJulia/BioJulia

🧬 SECTION 18 — Experimental Biology Automation

  1. opentrons/opentrons
  2. OpenLabware/OpenLabware
  3. PyLabRobot/PyLabRobot
  4. LabAutomation/LabAutomation
  5. Benchling/benchling-api
  6. Aquarium/aquarium
  7. Autoprotocol/autoprotocol
  8. Antha/antha
  9. OpentronsProtocolLibrary
  10. LabThings/labthings

🧬 SECTION 19 — Knowledge Graphs for Cancer Research

  1. Hetionet/hetionet
  2. BioKG/BioKG
  3. MonarchInitiative/monarch-app
  4. ROBOKOP/ROBOKOP
  5. SPOKE/SPOKE
  6. RTX/RTX
  7. Bio2RDF/Bio2RDF
  8. INDRA/INDRA
  9. Neo4j-Genomics/Neo4jGenomics
  10. KnowledgeGraph-Bio/KG-Bio

🧠 Important Reality Insight

In real frontier cancer research, >90% of pipelines combine:

Nextflow/Snakemake pipelines
+ GATK / RNA-seq tools
+ Seurat single-cell analysis
+ Immune deconvolution tools
+ AI drug discovery frameworks

This ecosystem forms the modern computational oncology stack.