From 783d416ecbb490e6c93da7b634edbcbc7fd1a3c7 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Fri, 17 Jul 2026 21:13:48 +0000 Subject: [PATCH 1/4] [upstream-sync] README.md from inoue0426/awesome-computational-biology@478be843 [catalogue] --- .../catalogue/README.md | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/README.md b/upstream/inoue0426-awesome-computational-biology/catalogue/README.md index 42bfd3d..cc9edd8 100644 --- a/upstream/inoue0426-awesome-computational-biology/catalogue/README.md +++ b/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/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 -- 2.54.0 From 86a74a726b0850d26d10311e430d4263d6569d71 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Fri, 17 Jul 2026 21:13:57 +0000 Subject: [PATCH 2/4] [upstream-sync] data/resources.json from inoue0426/awesome-computational-biology@478be843 [catalogue] --- .../catalogue/data/resources.json | 134 +++++++++++++++++- 1 file changed, 131 insertions(+), 3 deletions(-) diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.json b/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.json index 99b761c..5130edb 100644 --- a/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.json +++ b/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/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", -- 2.54.0 From 34f5e0887c0b2229786583262413e2c58172f537 Mon Sep 17 00:00:00 2001 From: promptadmin Date: Fri, 17 Jul 2026 21:14:07 +0000 Subject: [PATCH 3/4] [upstream-sync] data/resources.yml from inoue0426/awesome-computational-biology@478be843 [catalogue] --- .../catalogue/data/resources.yml | 83 ++++++++++++++++++- 1 file changed, 80 insertions(+), 3 deletions(-) diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.yml b/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.yml index 4bd0311..270b724 100644 --- a/upstream/inoue0426-awesome-computational-biology/catalogue/data/resources.yml +++ b/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/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 -- 2.54.0 From 1601315615b74ec1a131f5c07946a023f66da43c Mon Sep 17 00:00:00 2001 From: promptadmin Date: Fri, 17 Jul 2026 21:14:17 +0000 Subject: [PATCH 4/4] [upstream-sync] docs/data/resources.json from inoue0426/awesome-computational-biology@478be843 [catalogue] --- .../catalogue/docs/data/resources.json | 134 +++++++++++++++++- 1 file changed, 131 insertions(+), 3 deletions(-) diff --git a/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/resources.json b/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/resources.json index dfee624..f001590 100644 --- a/upstream/inoue0426-awesome-computational-biology/catalogue/docs/data/resources.json +++ b/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/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", -- 2.54.0