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

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