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Update HCA preview data gene counting matrix #23

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a7e967a
Update HCA preview data gene counting matrix
LuyiTian Apr 27, 2018
eef852c
Added direct download links.
batson May 1, 2018
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5 changes: 3 additions & 2 deletions README.md
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Expand Up @@ -5,7 +5,7 @@ Easy access to a small collection of benchmark datasets for methods development.

<p align="center">
<a href="benchmarks.md">Why do we need data benchmarks?</a>&nbsp;&nbsp;&nbsp;
<a href="contributing.md">Contribution guide</a>&nbsp;&nbsp;&nbsp;
<a href="CONTRIBUTING.md">Contribution guide</a>&nbsp;&nbsp;&nbsp;
</p>

## Contents
Expand All @@ -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

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20 changes: 20 additions & 0 deletions datasets/HCA_preview_scPipe.md
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# 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/<dataset_name>/gene_count.csv.zip`. Quality control metrics generated by scPipe during data preprocessing can be found in `data/<dataset_name>/stat`