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Code accompanying White et al. 2017
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dataFiles
.gitignore
GO-biolayout.md
LICENSE.txt
README.md
make_go_zfa_summary.R
parse_GO_results.pl
sample_strip.pl
topGO-multiple-clusters.R
zfa-enrichment.md
zfs-devstages.Rproj
zfs-plots.Rmd
zfs-plots.html

README.md

This code is associated with the paper from White et al., "A high-resolution mRNA expression time course of embryonic development in zebrafish". eLife, 2017. http://dx.doi.org/10.7554/eLife.30860

Notes to recreate the analysis in White et al. 2017

Contents

  • GO-biolayout.md Notes on running topGO on the gene clusters created using BioLayout Express
  • zfs-plots.Rmd Rmarkdown file to reproduce the plots in the paper

Counts Files

The zfs-plots Rmarkdown file expects two data files which do not exist in the repository for reasons of size. To run the code you will need to first download the files below

  • RNA-seq count data
    Download from Figshare
    This needs to be named zfs-rnaseq-grcz10.tsv and put in the dataFiles/rnaseq/ directory

  • DeTCT count data
    Download from Figshare
    This needs to be named zfs-detct-grcz10.tsv and put in the dataFiles/detct/ directory

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