the platform

Datasets

Public, version-controlled, gold-standard datasets used to evaluate methods across the benchmarks.

showing 81 datasets

1 MB

10X Post Xenium - Human Colon

Gene expression library of Post Xenium Human Colon Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set - Replicate 1

used in 1 task
1 MB

10X Post Xenium - Mouse Brain

Gene expression library of Post Xenium Mouse Brain (CytAssist Fresh Frozen) using the Mouse Whole Transcriptome Probe Set - Replicate 1

used in 1 task
1 MB

10X Visium - Adult Human Cerebellum

Human Cerebellum Whole Transcriptome Analysis

used in 1 task
1 MB

10X Visium - Human Brain Cancer

Gene expression library of Human Glioblastoma (CytAssist FFPE) using the Human Whole Transcriptome Probe Set

used in 1 task
1 MB

10X Visium - Human Breast Cancer 1

Whole transcriptome analysis, Adult Human Breast Cancer (Visium)

used in 1 task
0 MB

10X Visium - Human Breast Cancer 2

Gene expression library of Human Breast Cancer (Visium FFPE) using the Human Whole Transcriptome Probe Set

used in 1 task
0 MB

10X Visium - Human Cervical Cancer

Gene expression library of Human Cervical Cancer (Visium FFPE) using the Human Whole Transcriptome Probe Set

used in 1 task
1 MB

10X Visium - Human Colorectal Cancer

Gene expression library of Human Colorectal Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set

used in 1 task
1 MB

10X Visium - Human Heart

V1_Human_Heart

used in 1 task
1 MB

10X Visium - Human Heart MI 1

Gene expression library of human heart using 10x Visium.

used in 1 task
1 MB

10X Visium - Human Heart MI 2

Gene expression library of human heart using 10x Visium.

used in 1 task
0 MB

10X Visium - Human Intestine Cancer

Gene expression library of Human Intestinal Cancer (Visium FFPE) using the Human Whole Transcriptome Probe Set

used in 1 task
1 MB

10X Visium - Human Kidney

Gene expression library of Human Kidney (CytAssist FFPE) using the Human Whole Transcriptome Probe Set

used in 1 task
1 MB

10X Visium - Human Lung Cancer

Gene expression library of Human Lung Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set

used in 1 task
0 MB

10X Visium - Human Lymph Node

Whole transcriptome analysis, Human Lymph Node

used in 1 task
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10X Visium - Human Normal Prostate

Gene expression library of Human Normal Prostate (Visium FFPE) using the Human Whole Transcriptome Probe Set

used in 1 task
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10X Visium - Human Prostate Cancer

Gene expression library of Human Prostate Cancer (Visium FFPE) with an IF image using the Human Whole Transcriptome Probe Set

used in 1 task
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10X Visium - Human Skin Melanoma

Gene expression library of Human Skin Melanoma (CytAssist FFPE) using the Human Whole Transcriptome Probe Set

used in 1 task
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10X Visium - Mouse Brain Coronal

Gene expression library of Mouse Brain (CytAssist FFPE) using the Mouse Whole Transcriptome Probe Set

used in 1 task
1 MB

10X Visium - Mouse Embryo

Gene expression library of Mouse Embryo (CytAssist FFPE) using the Mouse Whole Transcriptome Probe Set

used in 1 task
0 MB

10X Visium - Mouse Kidney 1

Mouse Kidney Whole Transcriptome Analysis

used in 1 task
0 MB

10X Visium - Mouse Olfactory Bulb

10X Genomics obtained fresh frozen mouse olfactory bulb tissue from BioIVT.

used in 1 task

1k Peripheral blood mononuclear cells

1k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in November 2018 by 10X Genomics.

used in 1 task

5k Peripheral blood mononuclear cells

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

used in 1 task

CITE-seq Cord Blood Mononuclear Cells

8k cord blood mononuclear cells sequenced by CITEseq, a multimodal addition to the 10x scRNA-seq platform that allows simultaneous measurement of RNA and protein.

used in 1 task
0 MB

DBiT-seq - Mouse Brain (E10)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.

used in 1 task
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DBiT-seq - Mouse Eye (E10)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.

used in 1 task
0 MB

DBiT-seq - Mouse Lower Body (E11)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.

used in 1 task
0 MB

DBiT-seq - Mouse Whole Body (E10)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.

used in 1 task
0 MB

DBiT-seq - Mouse Whole Body 1 (E11)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.

used in 1 task
0 MB

DBiT-seq - Mouse Whole Body 2 (E11)

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.

used in 1 task

DestVI

scRNA-seq is generated based on learn NB parameters from the destVI manuscripts leveraging sparsePCA. Number of cells and cell types present in each spatial spot is computed via combination of kernel-based parametrization of a categorical distribution and the NB model.

used in 1 task
418 MB

Diabetic Kidney Disease

Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression

used in 3 tasks
1.0 GB

GTEX v9

Single-nucleus cross-tissue molecular reference maps to decipher disease gene function

used in 3 tasks

HypoMap

A unified single cell gene expression atlas of the murine hypothalamus

used in 2 tasks

Immune Cell Atlas

Cross-tissue immune cell analysis reveals tissue-specific features in humans

used in 3 tasks
1 MB

MERFISH - Human Cortex 1

Spatially resolved profiling of human cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH).

used in 1 task
0 MB

MERFISH - Human Cortex 2

Spatially resolved profiling of human cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH).

used in 1 task
0 MB

MERFISH - Human Cortex 3

Spatially resolved profiling of human cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH).

used in 1 task
0 MB

MERFISH - Human Cortex 4

Spatially resolved profiling of human cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH).

used in 1 task
1 MB

MERFISH - Mouse Cortex

Spatially resolved profiling of mouse cerebral cortex using multiplexed error-robust fluorescence in situ hybridization (MERFISH).

used in 1 task

Mouse brain atlas

A murine brain atlas with adjacent cell types as assumed benchmark truth, inferred from deconvolution proportion correlations using matching 10x Visium slides (see Dimitrov et al., 2022). 14249 cells x 34617 features with 23 cell type labels.

used in 1 task

Mouse hematopoietic stem cell differentiation

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

used in 1 task

Mouse myeloid lineage differentiation

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

used in 1 task

Mouse Pancreatic Islet Atlas

Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes

used in 2 tasks
13 MB

NeurIPS2021 CITE-Seq (ADT2GEX)

Single-cell CITE-Seq (GEX+ADT) data collected from bone marrow mononuclear cells of 12 healthy human donors.

used in 1 task
1 MB

NeurIPS2021 CITE-Seq (GEX2ADT)

Single-cell CITE-Seq (GEX+ADT) data collected from bone marrow mononuclear cells of 12 healthy human donors.

used in 1 task
8 MB

NeurIPS2021 Multiome (ATAC2GEX)

Single-cell Multiome (GEX+ATAC) data collected from bone marrow mononuclear cells of 12 healthy human donors.

used in 1 task
31 MB

NeurIPS2021 Multiome (GEX2ATAC)

Single-cell Multiome (GEX+ATAC) data collected from bone marrow mononuclear cells of 12 healthy human donors.

used in 1 task
183 MB

NeurIPS2023 scPerturb DGE

Differential gene expression sign(logFC) * -log10(p-value) values after 24 hours of treatment with 144 compounds in human PBMCs

used in 1 task
33 MB

OpenProblems NeurIPS2022 CITE-Seq (ADT2GEX)

Single-cell CITE-Seq (GEX+ADT) data collected from bone marrow mononuclear cells of 12 healthy human donors.

used in 1 task
1 MB

OpenProblems NeurIPS2022 CITE-Seq (GEX2ADT)

Single-cell CITE-Seq (GEX+ADT) data collected from bone marrow mononuclear cells of 12 healthy human donors.

used in 1 task

Pancreas (alpha=0.5)

Human pancreas cells aggregated from single-cell (Dirichlet alpha=0.5)

used in 1 task

Pancreas (alpha=1)

Human pancreas cells aggregated from single-cell (Dirichlet alpha=1)

used in 1 task

Pancreas (alpha=5)

Human pancreas cells aggregated from single-cell (Dirichlet alpha=5)

used in 1 task

Pancreas (inDrop)

Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). Here we just use the inDrop1 batch, which includes1937 cells × 15502 genes.

used in 1 task

sciCAR Cell Lines

5k cells from a time-series of dexamethasone treatment sequenced by sci-CAR, a combinatorial indexing-based co-assay that jointly profiles chromatin accessibility and mRNA.

used in 1 task

sciCAR Mouse Kidney

11k cells from adult mouse kidney sequenced by sci-CAR, a combinatorial indexing-based co-assay that jointly profiles chromatin accessibility and mRNA.

used in 1 task
1 MB

Seqfish - Mouse Organogenesis

Single-cell spatial expression of mouse organogenesis.

used in 1 task
2 MB

Slide-seqV2 - Mouse Cerebellum

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.

used in 1 task
1 MB

Slide-seqV2 - Mouse Cortex

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.

used in 1 task
2 MB

Slide-seqV2 - Mouse Hippocampus Puck

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.

used in 1 task
1 MB

Slide-seqV2 - Mouse Olfactory Bulb Puck

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.

used in 1 task
1 MB

Slide-seqV2 - Mouse Somatosensory Cortex Puck

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.

used in 1 task
0 MB

Slide-tags - Human Cortex

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.

used in 1 task
1 MB

Slide-tags - Human Skin Melanoma

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.

used in 1 task
1 MB

Slide-tags - Human Tonsil

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.

used in 1 task
1 MB

Slide-tags - Mouse Embryo

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics.

used in 1 task
0 MB

STARmap - Mouse Brain 1

Three-dimensional intact-tissue sequencing of single-cell transcriptional states.

used in 1 task
0 MB

STARmap - Mouse Brain 2

Three-dimensional intact-tissue sequencing of single-cell transcriptional states.

used in 1 task
0 MB

Stereo-seq - Drosophila embryo E10

Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution.

used in 1 task
0 MB

Stereo-seq - Drosophila embryo E5_6

Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution.

used in 1 task
0 MB

Stereo-seq - Drosophila embryo E6_3

Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution.

used in 1 task
0 MB

Stereo-seq - Drosophila embryo E7

Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution.

used in 1 task
0 MB

Stereo-seq - Drosophila embryo E9_1

Stereo-seq faithfully captures Drosophila spatial transcriptomes with high resolution.

used in 1 task

Tabula muris senis (alpha=0.5)

Mouse lung cells aggregated from single-cell (Dirichlet alpha=0.5)

used in 1 task

Tabula muris senis (alpha=1)

Mouse lung cells aggregated from single-cell (Dirichlet alpha=1)

used in 1 task

Tabula muris senis (alpha=5)

Mouse lung cells aggregated from single-cell (Dirichlet alpha=5)

used in 1 task

Tabula Muris Senis Lung

All lung cells from Tabula Muris Senis, a 500k cell-atlas from 18 organs and tissues across the mouse lifespan. Here we use just 10x data from lung. 24540 cells × 16160 genes across 3 time points.

used in 1 task

Tabula Sapiens

A multiple-organ, single-cell transcriptomic atlas of humans

used in 3 tasks

Zebrafish

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±1156 cells per cell type).

used in 1 task