Last updated: 2018-11-15

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✔ Repository version: 241c630

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File	Version	Author	Date	Message
Rmd	241c630	Lauren Blake	2018-07-05	Start workflowr project.

Welcome to my research notebook.

Data processing

Click here for a script to calculate the differences between blood collection dates.

Click here for a script to look at the names of the samples on flowcell 2.

This website has a good explanation about GENCODE annotations. Importantly, “In practical terms, the GENCODE annotation is identical to the Ensembl annotation.”

Click here for information about annotation files.

Global variation in the gene expression data

Click here for a global survey of the variation in gene expression data.

Exploring clinical covariates

Click here, here, and here to look at the correlations between covariates.

Lab changes over time can be found here.

To look at the relationship between self-reported race and ancestry, as well as race vs. genotype PCs, click here

Exploring weight over time

Weight changes over time can be found here.

Correlation between weight and other clinical covariates can be found here

Before and after nutritional rehabilitation: Differential expression/WGCNA/preparation for STEM:

Analysis with clinical covariates not including weight change as a covariate in the differential expression model.

Differential expression analysis using hg19/hg37

Differential expression analysis + DAVID input including weight change as a covariate.

To do:

Finish cleaning up covariate analysis (Preliminary_clinical_covariate.Rmd); Move flowcell technical factor analysis from import_transcript_level_estimates.Rmd.

Relationships between gene expression PCs and clinical covariates.

This reproducible R Markdown analysis was created with workflowr 1.1.1

Home

Data processing

Global variation in the gene expression data

Exploring clinical covariates

Exploring weight over time

Before and after nutritional rehabilitation: Differential expression/WGCNA/preparation for STEM: