Last updated: 2021-01-14

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Knit directory: esoph-micro-cancer-workflow/

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Rmd e6b4c7f noah-padgett 2021-01-14 meeting update
html e6b4c7f noah-padgett 2021-01-14 meeting update
Rmd 1d24c1f noah-padgett 2020-12-17 make waterfall-plots
html 1d24c1f noah-padgett 2020-12-17 make waterfall-plots
Rmd cf91029 noah-padgett 2020-12-02 updated analyses
html cf91029 noah-padgett 2020-12-02 updated analyses
Rmd 9937a7e noah-padgett 2020-11-05 new abundance data results
html 9937a7e noah-padgett 2020-11-05 new abundance data results
Rmd e41080d noah-padgett 2020-10-22 updated cleaning and ids data
html e41080d noah-padgett 2020-10-22 updated cleaning and ids data
html aaf0192 noah-padgett 2020-09-24 Build site.
Rmd ec3d151 noah-padgett 2020-09-24 updated processing files
Rmd 0159b72 noah-padgett 2020-09-23 initial commit
html 0159b72 noah-padgett 2020-09-23 initial commit

Welcome to our research website.

Data Pre-Processing

*NCI-UMD Data Process

*TCGA Data Process

*Sample IDs with Abundances

*Testing replication

*Waterfall Plots

*RNAscope test

Specific Questions for Update

Q1: is there a taxonomic signature shared between the barrett’s samples?

*Results Question 1

Q2: What is the abundance of F. nucleatum and/or Fusobacterium between these samples? - same samples as above

*Results Question 2

Q3: Is fuso associated with tumor stage in either data set? Does X bacteria predict stage? Multivariable w/ age, sex, BMI, history of Barrett’s

Add to this analysis: Fusobacterium nucleatum

Streptococcus sanguinis

Campylobacter concisus

Prevotella spp.

Same questions but using PICRUSt and HUMAnN data - Alison