[upstream-sync] docs/data/resources.json from inoue0426/awesome-computational-biology@478be843 [catalogue]

[upstream-sync] data/resources.yml from inoue0426/awesome-computational-biology@478be843 [catalogue]
[upstream-sync] data/resources.json from inoue0426/awesome-computational-biology@478be843 [catalogue]
2026-07-17 21:14:17 +00:00 · 2026-07-17 21:14:07 +00:00 · 2026-07-17 21:13:57 +00:00 · 2026-07-17 21:13:48 +00:00
4 changed files with 352 additions and 12 deletions
@@ -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/12d87583/README.md
-upstream_sha: 12d87583
-imported_at: 2026-06-26
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/478be843/README.md
+upstream_sha: 478be843
+imported_at: 2026-07-17
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -265,6 +265,8 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [Tabula Sapiens](https://tabula-sapiens-portal.ds.czbiohub.org/) — Comprehensive human single-cell atlas of ~500K cells from 24 organs and tissues across multiple donors.
 - [TAPE (Tasks Assessing Protein Embeddings)](https://github.com/songlab-cal/tape) — Benchmark suite of five biologically meaningful semi-supervised learning tasks for evaluating protein representations.
 - [The Cancer Genome Atlas (TCGA)](https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga) — Comprehensive multi-omics (genomics, transcriptomics, proteomics, methylation) dataset for 33 cancer types across ~11,000 patients.
+- [TCGA virtual spatial transcriptomics atlas](https://huggingface.co/datasets/ratschlab/TCGA_virtual_spatial_transcriptomics_atlas) — DeepSpot-M predicted transcriptome-wide ST for TCGA H&E (FF + FFPE; 28,664 slides / 32 cancer types; gated). Paper: [DeepSpot-M](https://www.medrxiv.org/content/10.64898/2026.06.19.26356060v1).
+- [HEST Xenium virtual spatial transcriptomics](https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics) — DeepSpot-M predicted transcriptome-wide ST for 59 HEST-1k 10x Xenium samples (~13.3M cells) (gated). Paper: [DeepSpot-M](https://www.medrxiv.org/content/10.64898/2026.06.19.26356060v1).
 - [Therapeutics Data Commons (TDC)](https://tdcommons.ai/) — Unified benchmark suite covering ADMET, drug-target interaction, drug response, and more.
 - [Tox21](https://tripod.nih.gov/tox21/challenge/) — 12,707 compounds tested in 12 nuclear receptor and stress-response pathway biochemical assays for toxicity prediction.
 - [UK Biobank](https://www.ukbiobank.ac.uk/) — Large-scale biomedical database of ~500K participants with genetic, imaging, and health data for population genetics and disease studies.
@@ -320,6 +322,7 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [sciPENN](https://github.com/jlakkis/sciPENN) — RNN-based method for simultaneous protein expression prediction, uncertainty estimation, and cell-type label transfer from CITE-seq and scRNA-seq data.
 - [MOGONET](https://github.com/txWang/MOGONET) — Multi-omics graph convolutional network framework for patient classification and biomarker identification.
 - [AutoZyme](https://github.com/ElliotXie/autozyme) — Autonomous agentic framework that speeds up bioinformatics software (e.g. Scanpy, Seurat) on CPUs while preserving the original results.
+- [SeqBench](https://seqbench.com/) — Web-based molecular biology sequence workbench for primer design, cloning simulation (Gibson, Golden Gate, restriction digest), CRISPR guide RNA design, and sequence analysis, with a public REST API, OpenAPI 3.1 spec, and MCP server.

 ---

@@ -412,6 +415,10 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [Phikon](https://huggingface.co/owkin/phikon) — ViT-based pathology foundation model pretrained with iBOT self-supervision on TCGA whole-slide images.
 - [Nicheformer](https://github.com/theislab/nicheformer) — Foundation model for single-cell and spatial omics using a transformer architecture with positional embeddings to encode spatial cell information.
 - [scGPT-spatial](https://github.com/bowang-lab/scGPT-spatial) — Extension of scGPT for spatial transcriptomics with continual pretraining and a mixture-of-experts decoder for spatial gene expression analysis.
+- [DeepSpot](https://github.com/ratschlab/DeepSpot) — Deep learning model predicting spatial transcriptomics from H&E images at spot and single-cell resolution.
+- [DeepSpot2Cell](https://github.com/ratschlab/DeepSpot2Cell) — Predicts virtual single-cell spatial transcriptomics from H&E using spot-level supervision (NeurIPS 2025 Imageomics).
+- [DeepSpot-M](https://github.com/ratschlab/DeepSpotM) — Multimodal foundation model for transcriptome-wide virtual spatial transcriptomics from histology.
+- [AESTETIK](https://github.com/ratschlab/aestetik) — Autoencoder for spatial transcriptomics representation learning using topology and histology image knowledge.

 ##### Multi-Omics Foundation Models

@@ -2,9 +2,9 @@
 title: "Resources"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/12d87583/data/resources.json
-upstream_sha: 12d87583
-imported_at: 2026-06-26
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/478be843/data/resources.json
+upstream_sha: 478be843
+imported_at: 2026-07-17
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -292,6 +292,20 @@ validated: false
    "organism": [],
    "api": false
  },
+  {
+    "id": "hest_xenium_virtual_spatial_transcriptomics",
+    "name": "HEST Xenium virtual spatial transcriptomics",
+    "type": "benchmark",
+    "url": "https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics",
+    "description": "DeepSpot-M predicted transcriptome-wide ST for 59 HEST-1k 10x Xenium samples (~13.3M cells) (gated). Paper: [DeepSpot-M](https://www.medrxiv.org/content/10.64898/2026.06.19.26356060v1).",
+    "tags": [
+      "benchmarks-and-datasets"
+    ],
+    "tasks": [],
+    "modalities": [],
+    "organism": [],
+    "api": false
+  },
  {
    "id": "jump_cell_painting_datasets",
    "name": "JUMP Cell Painting Datasets",
@@ -530,6 +544,20 @@ validated: false
    "organism": [],
    "api": false
  },
+  {
+    "id": "tcga_virtual_spatial_transcriptomics_atlas",
+    "name": "TCGA virtual spatial transcriptomics atlas",
+    "type": "benchmark",
+    "url": "https://huggingface.co/datasets/ratschlab/TCGA_virtual_spatial_transcriptomics_atlas",
+    "description": "DeepSpot-M predicted transcriptome-wide ST for TCGA H&E (FF + FFPE; 28,664 slides / 32 cancer types; gated). Paper: [DeepSpot-M](https://www.medrxiv.org/content/10.64898/2026.06.19.26356060v1).",
+    "tags": [
+      "benchmarks-and-datasets"
+    ],
+    "tasks": [],
+    "modalities": [],
+    "organism": [],
+    "api": false
+  },
  {
    "id": "the_cancer_genome_atlas_tcga",
    "name": "The Cancer Genome Atlas (TCGA)",
@@ -2095,6 +2123,27 @@ validated: false
    "organism": [],
    "api": false
  },
+  {
+    "id": "aestetik",
+    "name": "AESTETIK",
+    "type": "model",
+    "url": "https://github.com/ratschlab/aestetik",
+    "description": "Autoencoder for spatial transcriptomics representation learning using topology and histology image knowledge.",
+    "tags": [
+      "foundation-models",
+      "single-cell-foundation-models",
+      "spatial-foundation-models"
+    ],
+    "tasks": [
+      "Foundation Model"
+    ],
+    "modalities": [
+      "Single Cell",
+      "Spatial Transcriptomics"
+    ],
+    "organism": [],
+    "api": false
+  },
  {
    "id": "ai4chem_chemllm_7b_chat",
    "name": "AI4Chem/ChemLLM-7B-Chat",
@@ -2667,6 +2716,69 @@ validated: false
    "organism": [],
    "api": false
  },
+  {
+    "id": "deepspot",
+    "name": "DeepSpot",
+    "type": "model",
+    "url": "https://github.com/ratschlab/DeepSpot",
+    "description": "Deep learning model predicting spatial transcriptomics from H&E images at spot and single-cell resolution.",
+    "tags": [
+      "foundation-models",
+      "single-cell-foundation-models",
+      "spatial-foundation-models"
+    ],
+    "tasks": [
+      "Foundation Model"
+    ],
+    "modalities": [
+      "Single Cell",
+      "Spatial Transcriptomics"
+    ],
+    "organism": [],
+    "api": false
+  },
+  {
+    "id": "deepspot_m",
+    "name": "DeepSpot-M",
+    "type": "model",
+    "url": "https://github.com/ratschlab/DeepSpotM",
+    "description": "Multimodal foundation model for transcriptome-wide virtual spatial transcriptomics from histology.",
+    "tags": [
+      "foundation-models",
+      "single-cell-foundation-models",
+      "spatial-foundation-models"
+    ],
+    "tasks": [
+      "Foundation Model"
+    ],
+    "modalities": [
+      "Single Cell",
+      "Spatial Transcriptomics"
+    ],
+    "organism": [],
+    "api": false
+  },
+  {
+    "id": "deepspot2cell",
+    "name": "DeepSpot2Cell",
+    "type": "model",
+    "url": "https://github.com/ratschlab/DeepSpot2Cell",
+    "description": "Predicts virtual single-cell spatial transcriptomics from H&E using spot-level supervision (NeurIPS 2025 Imageomics).",
+    "tags": [
+      "foundation-models",
+      "single-cell-foundation-models",
+      "spatial-foundation-models"
+    ],
+    "tasks": [
+      "Foundation Model"
+    ],
+    "modalities": [
+      "Single Cell",
+      "Spatial Transcriptomics"
+    ],
+    "organism": [],
+    "api": false
+  },
  {
    "id": "dgdrp",
    "name": "DGDRP",
@@ -4913,6 +5025,22 @@ validated: false
    "organism": [],
    "api": false
  },
+  {
+    "id": "seqbench",
+    "name": "SeqBench",
+    "type": "toolkit",
+    "url": "https://seqbench.com/",
+    "description": "Web-based molecular biology sequence workbench for primer design, cloning simulation (Gibson, Golden Gate, restriction digest), CRISPR guide RNA design, and sequence analysis, with a public REST API, OpenAPI 3.1 spec, and MCP server.",
+    "tags": [
+      "preprocessing-tools"
+    ],
+    "tasks": [
+      "Preprocessing"
+    ],
+    "modalities": [],
+    "organism": [],
+    "api": false
+  },
  {
    "id": "seurat",
    "name": "Seurat",
@@ -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/12d87583/data/resources.yml
-upstream_sha: 12d87583
-imported_at: 2026-06-26
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/478be843/data/resources.yml
+upstream_sha: 478be843
+imported_at: 2026-07-17
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -248,6 +248,17 @@ resources:
    organism: []
    api: false

+  - id: hest_xenium_virtual_spatial_transcriptomics
+    name: "HEST Xenium virtual spatial transcriptomics"
+    type: benchmark
+    url: https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics
+    description: "DeepSpot-M predicted transcriptome-wide ST for 59 HEST-1k 10x Xenium samples (~13.3M cells) (gated). Paper: [DeepSpot-M](https://www.medrxiv.org/content/10.64898/2026.06.19.26356060v1)."
+    tags: [benchmarks-and-datasets]
+    tasks: []
+    modalities: []
+    organism: []
+    api: false
+
  - id: jump_cell_painting_datasets
    name: "JUMP Cell Painting Datasets"
    type: benchmark
@@ -435,6 +446,17 @@ resources:
    organism: []
    api: false

+  - id: tcga_virtual_spatial_transcriptomics_atlas
+    name: "TCGA virtual spatial transcriptomics atlas"
+    type: benchmark
+    url: https://huggingface.co/datasets/ratschlab/TCGA_virtual_spatial_transcriptomics_atlas
+    description: "DeepSpot-M predicted transcriptome-wide ST for TCGA H&E (FF + FFPE; 28,664 slides / 32 cancer types; gated). Paper: [DeepSpot-M](https://www.medrxiv.org/content/10.64898/2026.06.19.26356060v1)."
+    tags: [benchmarks-and-datasets]
+    tasks: []
+    modalities: []
+    organism: []
+    api: false
+
  - id: the_cancer_genome_atlas_tcga
    name: "The Cancer Genome Atlas (TCGA)"
    type: benchmark
@@ -1491,6 +1513,17 @@ resources:
    organism: []
    api: false

+  - id: aestetik
+    name: "AESTETIK"
+    type: model
+    url: https://github.com/ratschlab/aestetik
+    description: "Autoencoder for spatial transcriptomics representation learning using topology and histology image knowledge."
+    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
+    tasks: [Foundation Model]
+    modalities: [Single Cell, Spatial Transcriptomics]
+    organism: []
+    api: false
+
  - id: ai4chem_chemllm_7b_chat
    name: "AI4Chem/ChemLLM-7B-Chat"
    type: model
@@ -1810,6 +1843,39 @@ resources:
    organism: []
    api: false

+  - id: deepspot
+    name: "DeepSpot"
+    type: model
+    url: https://github.com/ratschlab/DeepSpot
+    description: "Deep learning model predicting spatial transcriptomics from H&E images at spot and single-cell resolution."
+    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
+    tasks: [Foundation Model]
+    modalities: [Single Cell, Spatial Transcriptomics]
+    organism: []
+    api: false
+
+  - id: deepspot_m
+    name: "DeepSpot-M"
+    type: model
+    url: https://github.com/ratschlab/DeepSpotM
+    description: "Multimodal foundation model for transcriptome-wide virtual spatial transcriptomics from histology."
+    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
+    tasks: [Foundation Model]
+    modalities: [Single Cell, Spatial Transcriptomics]
+    organism: []
+    api: false
+
+  - id: deepspot2cell
+    name: "DeepSpot2Cell"
+    type: model
+    url: https://github.com/ratschlab/DeepSpot2Cell
+    description: "Predicts virtual single-cell spatial transcriptomics from H&E using spot-level supervision (NeurIPS 2025 Imageomics)."
+    tags: [foundation-models, single-cell-foundation-models, spatial-foundation-models]
+    tasks: [Foundation Model]
+    modalities: [Single Cell, Spatial Transcriptomics]
+    organism: []
+    api: false
+
  - id: dgdrp
    name: "DGDRP"
    type: model
@@ -3097,6 +3163,17 @@ resources:
    organism: []
    api: false

+  - id: seqbench
+    name: "SeqBench"
+    type: toolkit
+    url: https://seqbench.com/
+    description: "Web-based molecular biology sequence workbench for primer design, cloning simulation (Gibson, Golden Gate, restriction digest), CRISPR guide RNA design, and sequence analysis, with a public REST API, OpenAPI 3.1 spec, and MCP server."
+    tags: [preprocessing-tools]
+    tasks: [Preprocessing]
+    modalities: []
+    organism: []
+    api: false
+
  - id: seurat
    name: "Seurat"
    type: toolkit
@@ -2,9 +2,9 @@
 title: "Resources"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/12d87583/docs/data/resources.json
-upstream_sha: 12d87583
-imported_at: 2026-06-26
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/478be843/docs/data/resources.json
+upstream_sha: 478be843
+imported_at: 2026-07-17
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -292,6 +292,20 @@ validated: false
    "organism": [],
    "api": false
  },
+  {
+    "id": "hest_xenium_virtual_spatial_transcriptomics",
+    "name": "HEST Xenium virtual spatial transcriptomics",
+    "type": "benchmark",
+    "url": "https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics",
+    "description": "DeepSpot-M predicted transcriptome-wide ST for 59 HEST-1k 10x Xenium samples (~13.3M cells) (gated). Paper: [DeepSpot-M](https://www.medrxiv.org/content/10.64898/2026.06.19.26356060v1).",
+    "tags": [
+      "benchmarks-and-datasets"
+    ],
+    "tasks": [],
+    "modalities": [],
+    "organism": [],
+    "api": false
+  },
  {
    "id": "jump_cell_painting_datasets",
    "name": "JUMP Cell Painting Datasets",
@@ -530,6 +544,20 @@ validated: false
    "organism": [],
    "api": false
  },
+  {
+    "id": "tcga_virtual_spatial_transcriptomics_atlas",
+    "name": "TCGA virtual spatial transcriptomics atlas",
+    "type": "benchmark",
+    "url": "https://huggingface.co/datasets/ratschlab/TCGA_virtual_spatial_transcriptomics_atlas",
+    "description": "DeepSpot-M predicted transcriptome-wide ST for TCGA H&E (FF + FFPE; 28,664 slides / 32 cancer types; gated). Paper: [DeepSpot-M](https://www.medrxiv.org/content/10.64898/2026.06.19.26356060v1).",
+    "tags": [
+      "benchmarks-and-datasets"
+    ],
+    "tasks": [],
+    "modalities": [],
+    "organism": [],
+    "api": false
+  },
  {
    "id": "the_cancer_genome_atlas_tcga",
    "name": "The Cancer Genome Atlas (TCGA)",
@@ -2095,6 +2123,27 @@ validated: false
    "organism": [],
    "api": false
  },
+  {
+    "id": "aestetik",
+    "name": "AESTETIK",
+    "type": "model",
+    "url": "https://github.com/ratschlab/aestetik",
+    "description": "Autoencoder for spatial transcriptomics representation learning using topology and histology image knowledge.",
+    "tags": [
+      "foundation-models",
+      "single-cell-foundation-models",
+      "spatial-foundation-models"
+    ],
+    "tasks": [
+      "Foundation Model"
+    ],
+    "modalities": [
+      "Single Cell",
+      "Spatial Transcriptomics"
+    ],
+    "organism": [],
+    "api": false
+  },
  {
    "id": "ai4chem_chemllm_7b_chat",
    "name": "AI4Chem/ChemLLM-7B-Chat",
@@ -2667,6 +2716,69 @@ validated: false
    "organism": [],
    "api": false
  },
+  {
+    "id": "deepspot",
+    "name": "DeepSpot",
+    "type": "model",
+    "url": "https://github.com/ratschlab/DeepSpot",
+    "description": "Deep learning model predicting spatial transcriptomics from H&E images at spot and single-cell resolution.",
+    "tags": [
+      "foundation-models",
+      "single-cell-foundation-models",
+      "spatial-foundation-models"
+    ],
+    "tasks": [
+      "Foundation Model"
+    ],
+    "modalities": [
+      "Single Cell",
+      "Spatial Transcriptomics"
+    ],
+    "organism": [],
+    "api": false
+  },
+  {
+    "id": "deepspot_m",
+    "name": "DeepSpot-M",
+    "type": "model",
+    "url": "https://github.com/ratschlab/DeepSpotM",
+    "description": "Multimodal foundation model for transcriptome-wide virtual spatial transcriptomics from histology.",
+    "tags": [
+      "foundation-models",
+      "single-cell-foundation-models",
+      "spatial-foundation-models"
+    ],
+    "tasks": [
+      "Foundation Model"
+    ],
+    "modalities": [
+      "Single Cell",
+      "Spatial Transcriptomics"
+    ],
+    "organism": [],
+    "api": false
+  },
+  {
+    "id": "deepspot2cell",
+    "name": "DeepSpot2Cell",
+    "type": "model",
+    "url": "https://github.com/ratschlab/DeepSpot2Cell",
+    "description": "Predicts virtual single-cell spatial transcriptomics from H&E using spot-level supervision (NeurIPS 2025 Imageomics).",
+    "tags": [
+      "foundation-models",
+      "single-cell-foundation-models",
+      "spatial-foundation-models"
+    ],
+    "tasks": [
+      "Foundation Model"
+    ],
+    "modalities": [
+      "Single Cell",
+      "Spatial Transcriptomics"
+    ],
+    "organism": [],
+    "api": false
+  },
  {
    "id": "dgdrp",
    "name": "DGDRP",
@@ -4913,6 +5025,22 @@ validated: false
    "organism": [],
    "api": false
  },
+  {
+    "id": "seqbench",
+    "name": "SeqBench",
+    "type": "toolkit",
+    "url": "https://seqbench.com/",
+    "description": "Web-based molecular biology sequence workbench for primer design, cloning simulation (Gibson, Golden Gate, restriction digest), CRISPR guide RNA design, and sequence analysis, with a public REST API, OpenAPI 3.1 spec, and MCP server.",
+    "tags": [
+      "preprocessing-tools"
+    ],
+    "tasks": [
+      "Preprocessing"
+    ],
+    "modalities": [],
+    "organism": [],
+    "api": false
+  },
  {
    "id": "seurat",
    "name": "Seurat",
Author	SHA1	Message	Date
promptadmin	1601315615	[upstream-sync] docs/data/resources.json from inoue0426/awesome-computational-biology@478be843 [catalogue]	2026-07-17 21:14:17 +00:00
promptadmin	34f5e0887c	[upstream-sync] data/resources.yml from inoue0426/awesome-computational-biology@478be843 [catalogue]	2026-07-17 21:14:07 +00:00
promptadmin	86a74a726b	[upstream-sync] data/resources.json from inoue0426/awesome-computational-biology@478be843 [catalogue]	2026-07-17 21:13:57 +00:00
promptadmin	783d416ecb	[upstream-sync] README.md from inoue0426/awesome-computational-biology@478be843 [catalogue]	2026-07-17 21:13:48 +00:00