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hagenaue / bHRbLR_Enrichment_Stress_BehaviorAndHormoneData

Code used for the analysis of behavioral and hormonal data within the publication "Adolescent environmental enrichment induces social resilience and alters neural gene expression in a selectively bred rodent model with anxious phenotype" by O'Connor, Hagenauer, et al.
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Background Reading: PCA & RNA-Seq #11

Open hagenaue opened 4 years ago

hagenaue commented 4 years ago

Attached is some background reading on Principal Components Analysis (PCA) and RNA-Sequencing.

hagenaue commented 4 years ago

Principal components analysis: I really like the general description given here: http://ordination.okstate.edu/PCA.htm This is a good interactive website: http://setosa.io/ev/principal-component-analysis/ Awesome introduction to matrix algebra: https://faculty.utrgv.edu/eleftherios.gkioulekas/Teaching/LectureNotes/MathForEEandLinAlg/books/book_tapia_linear_algebra.pdf

hagenaue commented 4 years ago

RNA-Seq background reading: I've attached a .pdf of a textbook: Next-Generation Sequencing Data Analysis by Wang (2016) Next-Gen_SequencingAnalysis.pdf

The first few chapters are mostly just a review of molecular biology (which you are probably already getting in your courses). These three chapters are probably the most applicable to our work:

Section II Introduction to Next-Generation Sequencing (NGS) and NGS Data Analysis

  1. Next-Generation Sequencing (NGS) Technologies: Ins and Outs
  2. Early-Stage Next-Generation Sequencing (NGS) Data Analysis: Common Steps

Section III Application-Specific NGS Data Analysis

  1. Transcriptomics by RNA-Seq