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

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upstream/inoue0426-awesome-computational-biology/catalogue/README.md
+12 -5
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@@ -2,9 +2,9 @@
title: "Awesome Computational Biology [![Awesome](https://awesome.re/badge.svg)](https://awesome.re)"
task: ""
lineage_type: import
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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
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@@ -2,9 +2,9 @@
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@@ -59,6 +59,7 @@ validated: false
"eukaryotic",
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@@ -171,7 +172,9 @@ validated: false
"bowang",
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upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.json
+430 -69
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@@ -2,9 +2,9 @@
title: "Resources"
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@@ -899,10 +899,20 @@ validated: false
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@@ -915,10 +925,20 @@ validated: false
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@@ -949,10 +978,20 @@ validated: false
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@@ -969,7 +1008,16 @@ validated: false
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@@ -983,11 +1031,22 @@ validated: false
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@@ -1000,10 +1059,20 @@ validated: false
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@@ -1016,10 +1085,19 @@ validated: false
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@@ -1032,10 +1110,23 @@ validated: false
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@@ -1092,10 +1183,20 @@ validated: false
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@@ -1124,10 +1225,19 @@ validated: false
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@@ -1141,11 +1251,20 @@ validated: false
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@@ -1174,10 +1293,21 @@ validated: false
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@@ -1208,10 +1338,21 @@ validated: false
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@@ -1225,11 +1366,19 @@ validated: false
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@@ -1292,10 +1441,21 @@ validated: false
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@@ -1308,10 +1468,20 @@ validated: false
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@@ -1349,10 +1519,20 @@ validated: false
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@@ -1365,10 +1545,19 @@ validated: false
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@@ -1936,6 +2125,22 @@ validated: false
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@@ -2383,10 +2588,18 @@ validated: false
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@@ -3995,7 +4208,7 @@ validated: false
"name": "MIDAS",
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"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": [
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@@ -4266,6 +4479,24 @@ validated: false
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},
{
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@@ -5444,9 +5675,23 @@ validated: false
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@@ -5476,9 +5721,22 @@ validated: false
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@@ -5492,9 +5750,20 @@ validated: false
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},
{
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@@ -5506,11 +5775,24 @@ validated: false
"preprocessing-tools"
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{
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@@ -5572,16 +5854,30 @@ validated: false
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@@ -5796,9 +6092,21 @@ validated: false
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},
{
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@@ -5812,9 +6120,22 @@ validated: false
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"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
+27 -5
View File
@@ -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_sha: 7a064bf0
imported_at: 2026-08-08
upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/data/resources.yml
upstream_sha: c6f07d90
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
+430 -69
View File
@@ -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/",
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