hhaiyu/singlecellseq

Batch effects and the effective design of single-cell gene expression studies

SingleCellSeq

Important links

See the site to view the results.

Read the paper.

Download the raw FASTQ files at GEO record GSE77288.

See the contributing guidelines to add a new analysis.

Project organization

• analysis/ contains the R Markdown files documenting the results
• paper/ contains the R Markdown files used to write the paper
• code/ contains command-line scripts
• data/ contains various summarized data files
• tests/ contains some sanity checks

The majority of the generated content, e.g. figures and HTML files, are in the analysis/ subdirectory of the gh-pages branch.

Useful data files

• reads.txt - tab-delimited file contains read counts for the 19,027 Ensembl protein-coding genes with at least one observed read in at least one of the 864 single cell samples
• molecules.txt - same as reads.txt, but for the molecule counts
• reads-filter.txt - tab-delimited file contains read counts for the 13,106 Ensembl protein-coding genes that passed our expression level filter for the 564 single cells that passed our quality control filters
• molecules-filter.txt - same as reads-filter.txt, but for the molecule counts
• molecules-final.txt - tab-delimited file contains the final gene expression values after all of our processing steps