upstream/inoue0426-awesome-computational-biology/catalogue/README.md

@@ -2,9 +2,9 @@
 title: "Awesome Computational Biology [![Awesome](https://awesome.re/badge.svg)](https://awesome.re)"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/README.md
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/README.md
-upstream_sha: 7a064bf0
+upstream_sha: c6f07d90
-imported_at: 2026-08-08
+imported_at: 2026-08-31
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -75,6 +75,7 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
       - [Drug Target Interaction](#drug-target-interaction)
       - [Compound-Protein Interaction](#compound-protein-interaction)
       - [Molecular Generation](#molecular-generation)
+    - [Protein Property Prediction](#protein-property-prediction)
     - [LLM for Biology](#llm-for-biology)
     - [Foundation Models](#foundation-models)
       - [Single-cell Foundation Models](#single-cell-foundation-models)
@@ -159,6 +160,7 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [GenBank](https://www.ncbi.nlm.nih.gov/genbank/) — NCBI's database of genetic sequences.
 - [UCSC Genome Browser](https://genome.ucsc.edu/) — UCSC's genome browser.
 - [cBioPortal](https://www.cbioportal.org/) — Cancer genomics database; aggregating many patient datasets.
+- [OncoKB](https://www.oncokb.org/) — Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.
 - [10x Genomics Dataset](https://www.10xgenomics.com/resources/datasets) — Collection of single-cell datasets.
 - [The Genotype-Tissue Expression (GTEx)](https://gtexportal.org/home/) — Human gene expression and regulation resource.
 - [Dependency Map (DepMap)](https://depmap.org/portal/) — CRISPR-Cas9 screens in cancer cell lines.
@@ -316,7 +318,7 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [CellCharter](https://github.com/CSOgroup/cellcharter) — Identification and characterization of spatial cell niches from spatial transcriptomics using VAEs and Gaussian mixture models.
 - [STAGATE](https://github.com/RucDongLab/STAGATE) — Adaptive graph attention auto-encoder for spatial domain identification in spatial transcriptomics.
 - [NCEM](https://github.com/theislab/ncem) — GNN-based model for learning intercellular communication from spatial graphs of cells.
-- [DeepTalk](https://github.com/JiangBioLab/DeepTalk) — Graph attention network for deciphering cell-cell communication from spatial transcriptomics data.
+- [DeepTalk](https://github.com/JiangBioLab/DeepTalk) — Graph attention network for deciphering cell-cell communication from spatial transcriptomics.
 - [COMMOT](https://github.com/zcang/COMMOT) — Optimal transport-based framework for screening cell-cell communication in spatial transcriptomics.
 - [TIGON](https://github.com/yutongo/TIGON) — Neural optimal transport method for reconstructing growth and dynamic trajectories from single-cell transcriptomics.
 - [LINGER](https://github.com/Durenlab/LINGER) — Neural network for gene regulatory network inference from single-cell multiome (RNA+ATAC-seq) data with bulk data pretraining.
@@ -383,6 +385,10 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [ReLeaSE](https://github.com/isayev/ReLeaSE) — Deep reinforcement learning framework for de novo drug design combining a generative and predictive model.
 - [PaccMannRL](https://github.com/PaccMann/paccmann_generator) — Reinforcement learning-based generative model for de novo hit-like anticancer molecule design from transcriptomic data.
 
+### Protein Property Prediction
+
+- [NbBayesLM](https://github.com/FairuzShadmaniShishir/NbBayesLM) — 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)
+
 ### LLM for Biology
 
 - [AI4Chem/ChemLLM-7B-Chat](https://huggingface.co/AI4Chem/ChemLLM-7B-Chat) — LLM for chemical & molecular science.
@@ -439,7 +445,7 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [GeneCompass](https://github.com/xCompass-AI/GeneCompass) — Large-scale foundation model integrating DNA regulatory sequences and single-cell transcriptomics from 120M+ cells across multiple species for gene regulation prediction.
 - [UnitedNet](https://github.com/LiuLab-Bioelectronics-Harvard/UnitedNet) — Interpretable multi-task deep neural network for single-cell multi-omics integration spanning transcriptomics, chromatin accessibility, and proteomics.
 - [SpatialGlue](https://github.com/zhanglabtools/SpatialGlue) — Graph attention network for spatial multi-omics integration jointly embedding spatial transcriptomics with chromatin accessibility or proteomics.
-- [MIDAS](https://github.com/labomics/midas) — Mosaic integration and differential accessibility model for single-cell multi-omics data that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.
+- [MIDAS](https://github.com/labomics/midas) — Mosaic integration and differential accessibility model for single-cell multi-omics that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.
 - [Concerto](https://github.com/melobio/Concerto-reproducibility) — Contrastive self-supervised learning framework for single-cell multimodal data integration, batch correction, and reference-query mapping.
 - [scButterfly](https://github.com/BioX-NKU/scButterfly) — Dual-aligned variational autoencoder for single-cell cross-modality translation between paired and unpaired multiomics data.
 - [JAMIE](https://github.com/Oafish1/JAMIE) — Joint variational autoencoder for multimodal single-cell data imputation and embedding.
@@ -521,6 +527,7 @@ If you use this list in papers, slides, or documentation, please cite this repos
 To keep quality high, additions should meet all of the following:
 
 - The resource is trustworthy and relevant to computational biology.
+- The resource has clear value to the scope and audience of this collection; highly specialized resources with limited relevance beyond a narrow application context may be declined even when technically sound.
 - The primary link points to an official source (official docs, organization site, maintained repository, or official dataset page).
 - The resource has evidence of technical substance: ideally a peer-reviewed paper; at minimum a preprint or official technical documentation.
 - The description is factual and concise (no marketing copy).

upstream/inoue0426-awesome-computational-biology/catalogue/cspell.json

@@ -2,9 +2,9 @@
 title: "Cspell"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/cspell.json
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/cspell.json
-upstream_sha: 7a064bf0
+upstream_sha: c6f07d90
-imported_at: 2026-08-08
+imported_at: 2026-08-31
 prompt_class: unknown
 upstream_changes: accepted
 author: upstream
@@ -59,6 +59,7 @@ validated: false
     "eukaryotic",
     "metabolites",
     "OMIM",
+    "OncoKB",
     "Mendelian",
     "DisGeNET",
     "GWAS",
@@ -171,7 +172,9 @@ validated: false
     "bowang",
     "ctheodoris",
     "OpenAI",
-    "GPT"
+    "GPT",
+    "nanobody",
+    "thermostability"
   ],
   "ignorePaths": [
     "node_modules/**"

upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.json

@@ -2,9 +2,9 @@
 title: "Resources"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/resources.json
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/data/resources.json
-upstream_sha: 7a064bf0
+upstream_sha: c6f07d90
-imported_at: 2026-08-08
+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",
+      "chemical-structure",
-      "Small Molecule"
+      "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",
+      "genomics",
-      "Small Molecule"
+      "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",
+      "knowledge-graph"
-      "Small Molecule"
     ],
     "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",
+      "knowledge-graph"
-      "Small Molecule"
     ],
     "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",

upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.yml

@@ -2,9 +2,9 @@
 title: "Awesome Computational Biology - machine-readable resource list"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/resources.yml
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/data/resources.yml
-upstream_sha: 7a064bf0
+upstream_sha: c6f07d90
-imported_at: 2026-08-08
+imported_at: 2026-08-31
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -1183,6 +1183,17 @@ resources:
     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"
     type: database
@@ -2243,7 +2254,7 @@ resources:
     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, single-cell-foundation-models]
     tasks: [Foundation Model]
     modalities: [Multi-Omics, Single Cell]
@@ -2382,6 +2393,17 @@ resources:
     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"
     type: model
@@ -2980,7 +3002,7 @@ resources:
     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]
     tasks: [Preprocessing]
     modalities: []

upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/resources.json

@@ -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_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/docs/data/resources.json
-upstream_sha: 7a064bf0
+upstream_sha: c6f07d90
-imported_at: 2026-08-08
+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",
+      "chemical-structure",
-      "Small Molecule"
+      "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",
+      "genomics",
-      "Small Molecule"
+      "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",
+      "knowledge-graph"
-      "Small Molecule"
     ],
     "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",
+      "knowledge-graph"
-      "Small Molecule"
     ],
     "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",