Repository organization and workflow

1. UNIXworkflow - runs on The Texas Advanced Computing Center's (TACC) cluster 'Stampede'

2. data - mostly raw data and meta data, some results included

3. docs - my talk for the R-Ladies Buenos Aires group

4. scripts

   • 00_cpfiles.sh - a bash script for copying files into and out of this repo
   • 01_behavior.md - output of a knittable analysis script for wrangling the avoidance behavior data. The output is use for the Fig*.Rmd scripts that accompany each figure
     • Figures 1, 2, 3, 4, 5, 6, 7 - Because I had so many behavior figures and accompanying statistics, I created a Rmd script containing the code to make the figure and calculate the statistics. The data were generated in 01_behavior.Rmd.
   • 02_RNAseq.md - output of an knittable analysis of differential gene expression of RNA-seq data with DESeq2, GO-WMU, and WGCNA
   • 03_wgcna.R - R script for weighted gene co-expression network analysis
   • 04_ephys.Rmd - analysis of hippocampal electrophysiology to measure synaptic properties -- note: must be run from the R command line as knitting doesn't currently work well
   • 05_Ceolin.md - a replication of a recently published paper and a comparison to my own data
   • 06_GO_MWU - directory with data, code, and results for Gene Ontology analysis

5. results

   • In the R script accompanying this file, 08_results.md, I write the results section for my manuscript.
   • This document is an executable way for me to keep the results section under version control and with newest version of the figure.
   • I alternate between exporting the result to a md_document and a word_document for writing my thesis

Data availability

• NCBI: The raw sequencing data, the counts matrix, and meta data at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106595
• GitHub: A collection of RNA-seq datasets listed by GEO accession number https://github.com/raynamharris/MouseHippocampusRNAseqData

The forthcoming manuscript

This research has been written up as a chapter of my doctoral thesis called "Reproducible approaches for studying behavior and transcription in a mouse model for autism". It will be modified before submitting to a jounral for peer review and publishing. Stayed tuned for citation details and links. The current draft can be found here: https://raynamharris.github.io/Thesis/02_fmr1.

Citation

• For the NCBI data archive, include this inline: Accession: GSE106595
• For the GitHub data, code, and results repository cite
• For the paper: stay tuned!!