Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update Dimensionality Reduction results #326

Open
wants to merge 8 commits into
base: main
Choose a base branch
from
Open

Update Dimensionality Reduction results #326

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
ebfd418
Update dim_red task to v2 results
KaiWaldrant Mar 5, 2024
7400aad
Update changelog
KaiWaldrant Mar 5, 2024
ce9e6ba
Update CHANGELOG.md
KaiWaldrant Mar 5, 2024
b2d6b32
Merge branch 'main' into feature/dim-red/update-results
rcannood Mar 18, 2024
671f081
update results
rcannood Mar 18, 2024
148a961
Merge remote-tracking branch 'origin/main' into feature/dim-red/updat…
rcannood Mar 18, 2024
aa3e7a4
update results
rcannood Mar 18, 2024
605ab96
Merge remote-tracking branch 'origin/main' into feature/dim-red/updat…
rcannood Apr 22, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@

## MAJOR CHANGES

* Update Dimensionality Reduction task to OpenProblems v2 results (PR #326).

* Migrated the result scaling from R to JavaScript to allow dynamically updating the results (PR #332).

## MINOR CHANGES
Expand Down
186 changes: 137 additions & 49 deletions results/dimensionality_reduction/data/dataset_info.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,50 +1,138 @@
[
{
"dataset_name": "Mouse hematopoietic stem cell differentiation",
"image": "openproblems",
"data_url": "https://ndownloader.figshare.com/files/36088649",
"data_reference": "nestorowa2016single",
"dataset_summary": "1.6k hematopoietic stem and progenitor cells from mouse bone marrow. Sequenced by Smart-seq2. 1920 cells x 43258 features with 3 cell type labels",
"task_id": "dimensionality_reduction",
"commit_sha": "ff1feaf0b741ec05b10084319a1175dfbf5e6faa",
"dataset_id": "mouse_hspc_nestorowa2016",
"source_dataset_id": "openproblems_v1/mouse_hspc_nestorowa2016",
"implementation_url": "https://github.com/openproblems-bio/openproblems/blob/main/openproblems/tasks/dimensionality_reduction/datasets/mouse_hspc_nestorowa2016.py"
},
{
"dataset_name": "Mouse myeloid lineage differentiation",
"image": "openproblems",
"data_url": "https://figshare.com/ndownloader/files/36872214",
"data_reference": "olsson2016single",
"dataset_summary": "Myeloid lineage differentiation from mouse blood. Sequenced by SMARTseq in 2016 by Olsson et al. 660 cells x 112815 features with 4 cell type labels",
"task_id": "dimensionality_reduction",
"commit_sha": "ff1feaf0b741ec05b10084319a1175dfbf5e6faa",
"dataset_id": "olsson_2016_mouse_blood",
"source_dataset_id": "openproblems_v1/mouse_blood_olsson_labelled",
"implementation_url": "https://github.com/openproblems-bio/openproblems/blob/main/openproblems/tasks/dimensionality_reduction/datasets/mouse_blood_olsson_labelled.py"
},
{
"dataset_name": "5k Peripheral blood mononuclear cells",
"image": "openproblems",
"data_url": "https://ndownloader.figshare.com/files/25555739",
"data_reference": "10x2019pbmc",
"dataset_summary": "5k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in July 2019 by 10X Genomics. 5247 cells x 20822 features with no cell type labels",
"task_id": "dimensionality_reduction",
"commit_sha": "ff1feaf0b741ec05b10084319a1175dfbf5e6faa",
"dataset_id": "tenx_5k_pbmc",
"source_dataset_id": "openproblems_v1/tenx_5k_pbmc",
"implementation_url": "https://github.com/openproblems-bio/openproblems/blob/main/openproblems/tasks/dimensionality_reduction/datasets/tenx_5k_pbmc.py"
},
{
"dataset_name": "Zebrafish",
"image": "openproblems",
"data_url": "https://ndownloader.figshare.com/files/24566651?private_link=e3921450ec1bd0587870",
"data_reference": "wagner2018single",
"dataset_summary": "90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. Dimensions: 26022 cells, 25258 genes. 24 cell types (avg. 1084\u00b11156 cells per cell type).",
"task_id": "dimensionality_reduction",
"commit_sha": "ff1feaf0b741ec05b10084319a1175dfbf5e6faa",
"dataset_id": "zebrafish_labs",
"source_dataset_id": "openproblems_v1/zebrafish",
"implementation_url": "https://github.com/openproblems-bio/openproblems/blob/main/openproblems/tasks/dimensionality_reduction/datasets/zebrafish.py"
}
]
{
"task_id": "dimensionality_reduction",
"dataset_id": "openproblems_v1/zebrafish",
"dataset_name": "Zebrafish embryonic cells",
"dataset_summary": "Single-cell mRNA sequencing of zebrafish embryonic cells.",
"data_reference": "wagner2018single",
"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112294"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "openproblems_v1/tenx_1k_pbmc",
"dataset_name": "1k PBMCs",
"dataset_summary": "1k peripheral blood mononuclear cells from a healthy donor",
"data_reference": "10x2018pbmc",
"data_url": "https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "openproblems_v1/immune_cells",
"dataset_name": "Human immune",
"dataset_summary": "Human immune cells dataset from the scIB benchmarks",
"data_reference": "luecken2022benchmarking",
"data_url": "https://theislab.github.io/scib-reproducibility/dataset_immune_cell_hum.html"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "openproblems_v1/mouse_blood_olsson_labelled",
"dataset_name": "Mouse myeloid",
"dataset_summary": "Myeloid lineage differentiation from mouse blood",
"data_reference": "olsson2016single",
"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70245"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "openproblems_v1/pancreas",
"dataset_name": "Human pancreas",
"dataset_summary": "Human pancreas cells dataset from the scIB benchmarks",
"data_reference": "luecken2022benchmarking",
"data_url": "https://theislab.github.io/scib-reproducibility/dataset_pancreas.html"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "openproblems_v1/cengen",
"dataset_name": "CeNGEN",
"dataset_summary": "Complete Gene Expression Map of an Entire Nervous System",
"data_reference": "hammarlund2018cengen",
"data_url": "https://www.cengen.org"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "openproblems_v1/tenx_5k_pbmc",
"dataset_name": "5k PBMCs",
"dataset_summary": "5k peripheral blood mononuclear cells from a healthy donor",
"data_reference": "10x2019pbmc",
"data_url": "https://www.10xgenomics.com/resources/datasets/5-k-peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-with-cell-surface-proteins-v-3-chemistry-3-1-standard-3-1-0"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "openproblems_v1/allen_brain_atlas",
"dataset_name": "Mouse Brain Atlas",
"dataset_summary": "Adult mouse primary visual cortex",
"data_reference": "tasic2016adult",
"data_url": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "cellxgene_census/dkd",
"dataset_name": "Diabetic Kidney Disease",
"dataset_summary": "Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression",
"data_reference": "wilson2022multimodal",
"data_url": "https://cellxgene.cziscience.com/collections/b3e2c6e3-9b05-4da9-8f42-da38a664b45b"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "cellxgene_census/immune_cell_atlas",
"dataset_name": "Immune Cell Atlas",
"dataset_summary": "Cross-tissue immune cell analysis reveals tissue-specific features in humans",
"data_reference": "dominguez2022crosstissue",
"data_url": "https://cellxgene.cziscience.com/collections/62ef75e4-cbea-454e-a0ce-998ec40223d3"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "openproblems_v1/mouse_hspc_nestorowa2016",
"dataset_name": "Mouse HSPC",
"dataset_summary": "Haematopoeitic stem and progenitor cells from mouse bone marrow",
"data_reference": "nestorowa2016single",
"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81682"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "openproblems_v1/tnbc_wu2021",
"dataset_name": "Triple-Negative Breast Cancer",
"dataset_summary": "1535 cells from six fresh triple-negative breast cancer tumors.",
"data_reference": "wu2021single",
"data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118389"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "cellxgene_census/tabula_sapiens",
"dataset_name": "Tabula Sapiens",
"dataset_summary": "A multiple-organ, single-cell transcriptomic atlas of humans",
"data_reference": "consortium2022tabula",
"data_url": "https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "cellxgene_census/gtex_v9",
"dataset_name": "GTEX v9",
"dataset_summary": "Single-nucleus cross-tissue molecular reference maps to decipher disease gene function",
"data_reference": "eraslan2022singlenucleus",
"data_url": "https://cellxgene.cziscience.com/collections/a3ffde6c-7ad2-498a-903c-d58e732f7470"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "cellxgene_census/hcla",
"dataset_name": "Human Lung Cell Atlas",
"dataset_summary": "An integrated cell atlas of the human lung in health and disease (core)",
"data_reference": "sikkema2023integrated",
"data_url": "https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "cellxgene_census/mouse_pancreas_atlas",
"dataset_name": "Mouse Pancreatic Islet Atlas",
"dataset_summary": "Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes",
"data_reference": "hrovatin2023delineating",
"data_url": "https://cellxgene.cziscience.com/collections/296237e2-393d-4e31-b590-b03f74ac5070"
},
{
"task_id": "dimensionality_reduction",
"dataset_id": "cellxgene_census/hypomap",
"dataset_name": "HypoMap",
"dataset_summary": "A unified single cell gene expression atlas of the murine hypothalamus",
"data_reference": "steuernagel2022hypomap",
"data_url": "https://cellxgene.cziscience.com/collections/d86517f0-fa7e-4266-b82e-a521350d6d36"
}
]
Loading