[Upstream sync] inoue0426/awesome-computational-biology (github) — 0 added, 5 modified #91

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@@ -2,9 +2,9 @@
title: "Resources"
task: ""
lineage_type: import
upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/docs/data/resources.json
upstream_sha: 7a064bf0
imported_at: 2026-08-08
upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/docs/data/resources.json
upstream_sha: c6f07d90
imported_at: 2026-08-31
prompt_class: catalogue
upstream_changes: accepted
author: upstream
@@ -899,10 +899,20 @@ validated: false
],
"tasks": [],
"modalities": [
"Genomics"
"single-cell-rna-seq",
"genomics"
],
"organism": [],
"api": false
"api": false,
"entities": [
"cell",
"gene"
],
"documentation": "https://www.10xgenomics.com/resources/datasets",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://www.10xgenomics.com/resources/datasets"
]
},
{
"id": "alphafold_protein_structure_database",
@@ -915,10 +925,20 @@ validated: false
],
"tasks": [],
"modalities": [
"Protein"
"molecular-structure",
"protein-sequence"
],
"organism": [],
"api": false
"api": false,
"entities": [
"protein"
],
"documentation": "https://alphafold.ebi.ac.uk/api-docs",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://alphafold.ebi.ac.uk/",
"https://alphafold.ebi.ac.uk/api-docs"
]
},
{
"id": "bindingdb",
@@ -932,11 +952,20 @@ validated: false
],
"tasks": [],
"modalities": [
"Protein",
"Small Molecule"
"chemical-structure",
"molecular-structure"
],
"organism": [],
"api": false
"api": false,
"entities": [
"molecule",
"protein"
],
"documentation": "https://www.bindingdb.org/rwd/bind/index.jsp",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://www.bindingdb.org/rwd/bind/index.jsp"
]
},
{
"id": "biocyc",
@@ -949,10 +978,20 @@ validated: false
],
"tasks": [],
"modalities": [
"Pathway"
"genomics"
],
"organism": [],
"api": false
"api": false,
"entities": [
"gene",
"pathway",
"organism"
],
"documentation": "https://biocyc.org/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://biocyc.org/"
]
},
{
"id": "biogrid",
@@ -969,7 +1008,16 @@ validated: false
"Protein"
],
"organism": [],
"api": false
"api": false,
"entities": [
"gene",
"protein"
],
"documentation": "https://thebiogrid.org/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://thebiogrid.org/"
]
},
{
"id": "cancer_cell_line_encyclopedia",
@@ -983,11 +1031,22 @@ validated: false
],
"tasks": [],
"modalities": [
"Gene Expression",
"Small Molecule"
"genomics",
"transcriptomics"
],
"organism": [],
"api": false
"api": false,
"entities": [
"cell",
"gene",
"disease",
"drug"
],
"documentation": "https://sites.broadinstitute.org/ccle/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://sites.broadinstitute.org/ccle/"
]
},
{
"id": "catalogue_of_somatic_mutations_in_cancer_cosmic",
@@ -1000,10 +1059,20 @@ validated: false
],
"tasks": [],
"modalities": [
"Genomics"
"genomics"
],
"organism": [],
"api": false
"api": false,
"entities": [
"disease",
"gene",
"variant"
],
"documentation": "https://cancer.sanger.ac.uk/cosmic",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://cancer.sanger.ac.uk/cosmic"
]
},
{
"id": "cath_database",
@@ -1016,10 +1085,19 @@ validated: false
],
"tasks": [],
"modalities": [
"Protein"
"molecular-structure",
"protein-sequence"
],
"organism": [],
"api": false
"api": false,
"entities": [
"protein"
],
"documentation": "https://www.cathdb.info/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://www.cathdb.info/"
]
},
{
"id": "cbioportal",
@@ -1032,10 +1110,23 @@ validated: false
],
"tasks": [],
"modalities": [
"Genomics"
"genomics",
"clinical"
],
"organism": [],
"api": false
"api": false,
"entities": [
"disease",
"gene",
"variant"
],
"github": "https://github.com/cBioPortal/cbioportal",
"documentation": "https://www.cbioportal.org/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://www.cbioportal.org/",
"https://github.com/cBioPortal/cbioportal"
]
},
{
"id": "cellminer_cross_database_cellminercdb",
@@ -1092,10 +1183,20 @@ validated: false
],
"tasks": [],
"modalities": [
"Small Molecule"
"chemical-structure"
],
"organism": [],
"api": false
"api": false,
"entities": [
"compound",
"molecule",
"protein"
],
"documentation": "https://www.ebi.ac.uk/chembl/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://www.ebi.ac.uk/chembl/"
]
},
{
"id": "chemspider",
@@ -1124,10 +1225,19 @@ validated: false
],
"tasks": [],
"modalities": [
"Clinical"
"clinical"
],
"organism": [],
"api": false
"api": false,
"entities": [
"disease",
"drug"
],
"documentation": "https://clinicaltrials.gov/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://clinicaltrials.gov/"
]
},
{
"id": "comparative_toxicogenomics_database",
@@ -1141,11 +1251,20 @@ validated: false
],
"tasks": [],
"modalities": [
"Gene",
"Small Molecule"
"knowledge-graph"
],
"organism": [],
"api": false
"api": false,
"entities": [
"compound",
"gene",
"disease"
],
"documentation": "https://ctdbase.org/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://ctdbase.org/"
]
},
{
"id": "critical_assessment_of_structure_prediction_casp",
@@ -1174,10 +1293,21 @@ validated: false
],
"tasks": [],
"modalities": [
"Single Cell"
"single-cell-rna-seq",
"transcriptomics"
],
"organism": [],
"api": false
"api": false,
"entities": [
"cell",
"gene",
"tissue"
],
"documentation": "https://cellxgene.cziscience.com/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://cellxgene.cziscience.com/"
]
},
{
"id": "davis_kinase_inhibitors_db",
@@ -1208,10 +1338,21 @@ validated: false
],
"tasks": [],
"modalities": [
"Genomics"
"genomics"
],
"organism": [],
"api": false
"api": false,
"entities": [
"cell",
"gene",
"disease",
"drug"
],
"documentation": "https://depmap.org/portal/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://depmap.org/portal/"
]
},
{
"id": "dgidb",
@@ -1225,11 +1366,19 @@ validated: false
],
"tasks": [],
"modalities": [
"Gene",
"Small Molecule"
"knowledge-graph"
],
"organism": [],
"api": false
"api": false,
"entities": [
"drug",
"gene"
],
"documentation": "https://www.dgidb.org/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://www.dgidb.org/"
]
},
{
"id": "diseases",
@@ -1292,10 +1441,21 @@ validated: false
],
"tasks": [],
"modalities": [
"Knowledge Graph"
"knowledge-graph"
],
"organism": [],
"api": false
"api": false,
"entities": [
"drug",
"disease",
"gene",
"pathway"
],
"github": "https://github.com/SuLab/DrugMechDB",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://github.com/SuLab/DrugMechDB"
]
},
{
"id": "drug_repurposing_hub",
@@ -1308,10 +1468,20 @@ validated: false
],
"tasks": [],
"modalities": [
"Small Molecule"
"chemical-structure"
],
"organism": [],
"api": false
"api": false,
"entities": [
"drug",
"protein",
"disease"
],
"documentation": "https://repo-hub.broadinstitute.org/repurposing",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://repo-hub.broadinstitute.org/repurposing"
]
},
{
"id": "drugbank",
@@ -1349,10 +1519,20 @@ validated: false
],
"tasks": [],
"modalities": [
"Small Molecule"
"chemical-structure"
],
"organism": [],
"api": false
"api": false,
"entities": [
"drug",
"protein",
"disease"
],
"documentation": "https://drugcentral.org/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://drugcentral.org/"
]
},
{
"id": "drugtargetcommons",
@@ -1365,10 +1545,19 @@ validated: false
],
"tasks": [],
"modalities": [
"Small Molecule"
"chemical-structure"
],
"organism": [],
"api": false
"api": false,
"entities": [
"drug",
"protein"
],
"documentation": "https://drugtargetcommons.fimm.fi/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://drugtargetcommons.fimm.fi/"
]
},
{
"id": "encode",
@@ -1936,6 +2125,22 @@ validated: false
"organism": [],
"api": false
},
{
"id": "oncokb",
"name": "OncoKB",
"type": "database",
"url": "https://www.oncokb.org/",
"description": "Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.",
"tags": [
"genome"
],
"tasks": [],
"modalities": [
"Genomics"
],
"organism": [],
"api": false
},
{
"id": "open_targets_platform",
"name": "Open Targets Platform",
@@ -2383,10 +2588,18 @@ validated: false
],
"tasks": [],
"modalities": [
"Protein"
"protein-sequence"
],
"organism": [],
"api": false
"api": false,
"entities": [
"protein"
],
"documentation": "https://www.uniprot.org/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://www.uniprot.org/"
]
},
{
"id": "uniref",
@@ -3995,7 +4208,7 @@ validated: false
"name": "MIDAS",
"type": "model",
"url": "https://github.com/labomics/midas",
"description": "Mosaic integration and differential accessibility model for single-cell multi-omics data that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.",
"description": "Mosaic integration and differential accessibility model for single-cell multi-omics that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.",
"tags": [
"foundation-models",
"multi-omics-foundation-models",
@@ -4266,6 +4479,24 @@ validated: false
"organism": [],
"api": false
},
{
"id": "nbbayeslm",
"name": "NbBayesLM",
"type": "model",
"url": "https://github.com/FairuzShadmaniShishir/NbBayesLM",
"description": "Bayesian neural network integrating protein language model embeddings and physicochemical features to predict nanobody thermostability with uncertainty estimates. [Paper](https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1832968/full)",
"tags": [
"protein-property-prediction"
],
"tasks": [
"Protein Property Prediction"
],
"modalities": [
"Protein"
],
"organism": [],
"api": false
},
{
"id": "neodti",
"name": "NeoDTI",
@@ -5444,9 +5675,23 @@ validated: false
"tasks": [
"Preprocessing"
],
"modalities": [],
"modalities": [
"dna-sequence",
"protein-sequence"
],
"organism": [],
"api": false
"api": false,
"entities": [
"gene",
"protein"
],
"github": "https://github.com/biopython/biopython",
"documentation": "https://biopython.org/wiki/Documentation",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://github.com/biopython/biopython",
"https://biopython.org/"
]
},
{
"id": "casper",
@@ -5476,9 +5721,22 @@ validated: false
"tasks": [
"Preprocessing"
],
"modalities": [],
"modalities": [
"spatial-transcriptomics"
],
"organism": [],
"api": false
"api": false,
"entities": [
"cell",
"tissue"
],
"github": "https://github.com/CSOgroup/cellcharter",
"documentation": "https://cellcharter.readthedocs.io/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://github.com/CSOgroup/cellcharter",
"https://cellcharter.readthedocs.io/"
]
},
{
"id": "cellchat",
@@ -5492,9 +5750,20 @@ validated: false
"tasks": [
"Preprocessing"
],
"modalities": [],
"modalities": [
"single-cell-rna-seq"
],
"organism": [],
"api": false
"api": false,
"entities": [
"cell",
"gene"
],
"github": "https://github.com/sqjin/CellChat",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://github.com/sqjin/CellChat"
]
},
{
"id": "celltypist",
@@ -5506,11 +5775,24 @@ validated: false
"preprocessing-tools"
],
"tasks": [
"Preprocessing"
"cell-type-annotation"
],
"modalities": [
"single-cell-rna-seq"
],
"modalities": [],
"organism": [],
"api": false
"api": false,
"entities": [
"cell",
"gene"
],
"github": "https://github.com/Teichlab/celltypist",
"documentation": "https://celltypist.readthedocs.io/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://github.com/Teichlab/celltypist",
"https://celltypist.readthedocs.io/"
]
},
{
"id": "chatspatial",
@@ -5572,16 +5854,30 @@ validated: false
"tasks": [
"Preprocessing"
],
"modalities": [],
"modalities": [
"chemical-structure",
"molecular-structure"
],
"organism": [],
"api": false
"api": false,
"entities": [
"molecule",
"protein"
],
"github": "https://github.com/deepchem/deepchem",
"documentation": "https://deepchem.readthedocs.io/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://github.com/deepchem/deepchem",
"https://deepchem.readthedocs.io/"
]
},
{
"id": "deeptalk",
"name": "DeepTalk",
"type": "toolkit",
"url": "https://github.com/JiangBioLab/DeepTalk",
"description": "Graph attention network for deciphering cell-cell communication from spatial transcriptomics data.",
"description": "Graph attention network for deciphering cell-cell communication from spatial transcriptomics.",
"tags": [
"preprocessing-tools"
],
@@ -5796,9 +6092,21 @@ validated: false
"tasks": [
"Preprocessing"
],
"modalities": [],
"modalities": [
"chemical-structure"
],
"organism": [],
"api": false
"api": false,
"entities": [
"molecule"
],
"github": "https://github.com/rdkit/rdkit",
"documentation": "https://www.rdkit.org/docs/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://github.com/rdkit/rdkit",
"https://www.rdkit.org/docs/"
]
},
{
"id": "scanpy",
@@ -5812,9 +6120,22 @@ validated: false
"tasks": [
"Preprocessing"
],
"modalities": [],
"modalities": [
"single-cell-rna-seq"
],
"organism": [],
"api": false
"api": false,
"entities": [
"cell",
"gene"
],
"github": "https://github.com/scverse/scanpy",
"documentation": "https://scanpy.readthedocs.io/en/stable/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://github.com/scverse/scanpy",
"https://scanpy.readthedocs.io/en/stable/"
]
},
{
"id": "scenic",
@@ -5876,9 +6197,23 @@ validated: false
"tasks": [
"Preprocessing"
],
"modalities": [],
"modalities": [
"single-cell-rna-seq",
"multi-omics"
],
"organism": [],
"api": false
"api": false,
"entities": [
"cell",
"gene"
],
"github": "https://github.com/scverse/scvi-tools",
"documentation": "https://docs.scvi-tools.org/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://github.com/scverse/scvi-tools",
"https://docs.scvi-tools.org/"
]
},
{
"id": "seqbench",
@@ -5908,9 +6243,22 @@ validated: false
"tasks": [
"Preprocessing"
],
"modalities": [],
"modalities": [
"single-cell-rna-seq"
],
"organism": [],
"api": false
"api": false,
"entities": [
"cell",
"gene"
],
"github": "https://github.com/satijalab/seurat",
"documentation": "https://satijalab.org/seurat/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://github.com/satijalab/seurat",
"https://satijalab.org/seurat/"
]
},
{
"id": "squidpy",
@@ -5924,9 +6272,22 @@ validated: false
"tasks": [
"Preprocessing"
],
"modalities": [],
"modalities": [
"spatial-transcriptomics"
],
"organism": [],
"api": false
"api": false,
"entities": [
"cell",
"tissue"
],
"github": "https://github.com/scverse/squidpy",
"documentation": "https://squidpy.readthedocs.io/",
"last_checked": "2026-08-08",
"metadata_sources": [
"https://github.com/scverse/squidpy",
"https://squidpy.readthedocs.io/"
]
},
{
"id": "stagate",