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ALS implicated protein TDP-43 sustains levels of STMN2, a mediator of motor neuron growth and repair
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bcbio_config
bcbio_info
00_pinned_install.R
01_loadRNASeq.R
02_quality_control.Rmd
02_quality_control.html
03_differential_expression.Rmd
03_differential_expression.html
04_gene_plots.R
05_labeled_volcano_and_ma_plots.R
06_degreport.R
README.md
_footer.Rmd
_header.Rmd
_output.yaml
_setup.R
bibliography.bib
metadata.csv

README.md

ALS implicated protein TDP-43 sustains levels of STMN2, a mediator of motor neuron growth and repair

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.

Analysis scripts

  • 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.

Additional

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