easy-data

Easy access to a small collection of benchmark datasets for methods development.

Why do we need data benchmarks?    Contribution guide   

Contents

• Imaging
• Multiomics
• RNA-Seq

Datasets

Instructions for downloading and loading each dataset are in text files in the datasets folder.

RNA-Seq

• Loyale Developing mouse retina - 10x single cell RNA-seq data from the developing mouse retina. Code repo | Download instructions #retina #mouse #umi #10x #droplet
• Tabula Muris - 20 different mouse organs, both full transcript (SmartSeq2) and UMI-based droplet counting (10x Genomics). Code repo | Vignette repo | Interactive website | Download instructions #mouse #aorta #bladder #brain #diaphragm #fat #heart #kidney #large_intestine #muscle #liver #lung #mammary_gland #marrow #pancreas #skin #spleen #thymus #tongue #rnaseq #smartseq2 #10x #umi #droplet
• Human cortex development - 4000 SmartSeq2 cells from different locations of the developing human fetus.
• Conquer - 38 datasets summarized to a count level available as R MultiAssayExperiment objects.
• CellBench pilot data set - mixture data set from 3 human lung adenocarcinoma cell lines (HCC827, H1975 and H2228) across different platforms.

Imaging

• Example dataset - 1-2 sentence summary of dataset. Code Repo | Vignette Repo | Interactive Website | Download instructions #mouse

Multiomics

• Example dataset - 1-2 sentence summary of dataset. Code Repo | Vignette Repo | Interactive Website | Download instructions #mouse