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index.Rmd
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---
title: "Esophogus-Microbiome-Cancer"
site: workflowr::wflow_site
output:
workflowr::wflow_html:
toc: false
editor_options:
chunk_output_type: console
---
Welcome to our research website.
## Data Pre-Processing
*[NCI-UMD Data Process](data_processing_nci_umd.html)
*[TCGA Data Process](data_processing_tcga.html)
*[Sample IDs with Abundances](ids_abundance_misc.html)
*[Testing replication](test-of-replication.html)
*[Waterfall Plots](waterfall-plot.html)
*[RNAscope test](data-check-for-RNAscope.html)
## Abundance Data
Violin plots with abundance of each bacteria across samples with Barretts history.
*[Violin plots for bacterial abundance by Barretts samples](species-sample-type-combined.html)
The following pages give a variety of heatmaps w/ dendrograms that help describe the differences in OTU abundance across groups.
*[Genera Level Heatmaps with Dendrograms](slide-figures-heatmaps-dendrograms-updates.html)
*[Species Level Heatmaps with Dendrograms](heatmaps-dendrograms-species-level.html)
The following page helps describe the relationship between Fuso (and other OTUs) and tumor stage.
* Is fuso associated with tumor stage in either data set? Does X bacteria predict stage? Multivariable w/ age, sex, BMI, history of Barrett's
*[Ordered Logit Model Results](ordered-logit-model.html)
## Analyses
Bag-of-Genes Analyses
*[PICRUSt Results](picrust-analyses.html)
Results Stratified by Taxa
*[PICRUSt Results - Fusobacterium nucleatum](picrust-fuso.html)
*[PICRUSt Results - Streptococcus sanguinis](picrust-strepto.html)
*[PICRUSt Results - Campylobacter concisus](picrust-campy.html)
*[PICRUSt Results - Prevotella spp. (genus level only)](picrust-prevo.html)
Survival Analysis
*[Survival Analysis Results](survival-analysis.html)