Examination of the oral microbiome and cancer

The code and subset metadata files in this repository correspond to the following manuscript:

Nearing et al. Npj biofilms. Investigating the oral microbiome in retrospective and prospective cases of prostate, colon, and breast cancer.

Our goal with this work was to examine the differences in the oral microbiome of individuals that were reterospectively or prospectively diagnosised with breast, prostate, and colon cancer.

Repository organization

• Revised_Analyis_scripts contains the R scripts used to analysis 16S rRNA gene sequencing taxonomic tables. All data presented in the above corresponding paper was analysised by scripts within this folder. All scripts within this folder have their PATH directed to the data and resulting files location on local machines within the Langille Lab. These PATHs will need to editted to point to the data on your local machine.
• Data contains deidentified limited metadata for the samples that were examined for this paper. Raw sequencing data for these samples can be obtained here: PRJEB38175 and PRJEB56605. To access higher detail metadata please make a request to either Atlantic PATH or Alberta's Tommorrow Project