shell scripts, R scripts, and data required to reproduce the main analyses in Sokolowski et al., 2023

These directories contain the scripts (shell and R) and data required for the primary analysis of Sokolowski et al., 2023. Title: Transcriptomic effects of the foraging gene shed light on pathways of pleiotropy and plasticity. Athors: Authors: Dustin J. Sokolowski1,2*, Oscar E. Vasquez3*, Michael D. Wilson1,2, Marla B. Sokolowski3,4, Ina Anreiter5
Author Affiliations *Authors contributed equally 1Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada 2Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada 3Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada 4Program in Child and Brain Development, Canadian Institute for Advanced Research, ON, Canada. 5Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada Corresponding Author For Manuscript: ina-dot-anreiter-at-utoronto-dot-ca Data analysis and figshare generator: dustin-dot-sokolowski-at-sickkids-dot-ca - alternative email (for when moved on from PhD) - djsokolowski95-at-gmail-dot-com
Each folder has it's own readme explaining the contents within. Directories have not been changed. Therefore to re-generate any output, they would need to be switched for the indivudal The raw and processed data (outside of the fastq, bw, and bam files) to regenerate the major analyses of each paper are the in /data subdirectory already. This includes all of the DEGs, pathways, varimax genes, scMappR outputs, SNP vcf files etc.
The sequencing information associated with these data can be found on arrayexpress https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-12688?query=foraging
R packages used: - scMappR - DESeq2 - gplots - edgeR - reshape2 - ggplot2 - TxDb.Dmelanogaster.UCSC.dm6.ensGene - org.Dm.eg.db - ChIPseeker - ggfortify - scales - xlsx - ActivePathways - DEET - Seurat - WGCNA - pheatmap - gProfileR - dplyr - reshape
Genomics command-line modules used: - fastqc - STAR - trimmomatic - bwa - samtools - bedtools - bcftools - gatk (picard) - featurecounts - qualimap - DeepTools