Why do we need data benchmarks? - Contribution guide + Contribution guide
## Contents @@ -25,7 +25,8 @@ Instructions for downloading and loading each dataset are in text files in the ` - [Tabula Muris](datasets/tabula_muris.md) - 20 different mouse organs, both full transcript (SmartSeq2) and UMI-based droplet counting (10x Genomics). [Code repo](https://github.com/czbiohub/tabula-muris) | [Vignette repo](https://github.com/czbiohub/tabula-muris-vignettes) | [Interactive website](http://tabula-muris.ds.czbiohub.org/) | [Download instructions](datasets/tabula_muris.md) #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](datasets/ucsc_human_cortex.md) - 4000 SmartSeq2 cells from different locations of the developing human fetus. - [Conquer](datasets/conquer.md) - [38 datasets](http://imlspenticton.uzh.ch:3838/conquer/) summarized to a count level available as `R` `MultiAssayExperiment` objects. -- [CellBench pilot data set](https://github.com/LuyiTian/CellBench_data/blob/master/cellbench.md) - mixture data set from 3 human lung adenocarcinoma cell lines (HCC827, H1975 and H2228) across different platforms. +- [CellBench pilot data set](https://github.com/LuyiTian/CellBench_data/blob/master/cellbench.md) - mixture data set from 3 human lung adenocarcinoma cell lines (HCC827, H1975 and H2228) across different platforms. #benchmark #celseq2 #dropseq #10x #cellline +- [HCA preview dataset gene counting matrix](datasets/HCA_preview_scPipe.md) - HCA preview data gene counting matrix. The gene counting matrix was generated from fastq by [scPipe](https://bioconductor.org/packages/release/bioc/html/scPipe.html). #hca #scPipe ### Imaging diff --git a/datasets/HCA_preview_scPipe.md b/datasets/HCA_preview_scPipe.md new file mode 100644 index 0000000..8672841 --- /dev/null +++ b/datasets/HCA_preview_scPipe.md @@ -0,0 +1,20 @@ +# HCA_Previewdata +Mixture data set from 3 human lung adenocarcinoma cell lines (HCC827, H1975 and H2228) across different platforms: celseq2, dropseq, and 10x. + +Data was downloaded from [HCA data portal](https://preview.data.humancellatlas.org/) and processed in [this repo](https://github.com/LuyiTian/HCA_Previewdata) using scPipe. + +## Metadata + +Metadata is stored in [HCA data portal](https://preview.data.humancellatlas.org/) and can be downloaded directly [here](https://preview.data.humancellatlas.org/datasets/melanoma/hca-metadata-melanoma.xlsx). + +## Count files for R + +You can find SingleCellExperiment object for the dataset, either the [raw data](https://github.com/LuyiTian/HCA_Previewdata/blob/master/rdata/ischaemic_sensitivity_raw.RData?raw=true) or [processed data](https://github.com/LuyiTian/HCA_Previewdata/blob/master/rdata/ischaemic_sensitivity_QC_norm.RData) after quality control and normalization are in the `rdata` folder. + +## Exploratory data analysis + +Rmd document can be found in `script` folder. + +## CSV and MTX files + +You can find gene count matrix in `data/