Code for analysis of bcbio processed RNA-seq data using the bcbioRNASeq R package.

Contact Michael Steinbaugh for additional information.

Citation: Klim JR, Williams LA, Limone F, Guerra San Juan I, Davis-Dusenbery BN, Mordes DA, Burberry A, Steinbaugh MJ, Gamage KK, Kirchner R, Moccia R, Cassel SH, Chen K, Wainger BJ, Woolf CJ, Eggan K. (2019). ALS-implicated protein TDP-43 sustains levels of STMN2, a mediator of motor neuron growth and repair. Nat Neurosci.

• 00_pinned_install.R: R code to install pinned version of bcbioRNASeq.
• 01_loadRNASeq.R: R code to load bcbio processed RNA-seq data.
• 02_quality_control.Rmd: R Markdown code for quality control analysis.
• 03_differential_expression.Rmd: R Markdown code for differential expression analysis.
• 04_gene_plots.R: R code used to generate draft versions of gene expression plots.
• 05_labeled_volcano_and_ma_plots.R: R code used to generate draft versions of volcano and MA plots.
• 06_degreport.R: R code used to run additional quality control with DEGreport package.
• metadata.csv: Sample metadata.

• bcbio_config: Files used to configure bcbio run.
• bcbio_info: bcbio logs and data versions.