jjcolgan

Bodke-Script

Modified dada2 script, used for master's thesis project. Takes fast2 files and outputs ASV table, taxonomy table, phylogenetic tree, and input files for PICRUSt2

chimeraRemover

Removes chimeras from an ASV table using an input of asv table and a fasta file containing the chimeras

DataStructures

DrW_myrepo

group7Repo

Predictive model, utilizes several machine learning algorithms to predict patient disease status from abundance data

miniProject

NaRemover-

Remover ASVs with no taxonomic assignment. Takes dada2 output files (ASV and taxa table)

Revaluation-of-old-data-with-new-techniques-reveals-novel-insights-into-the-celiac-microbiome-

Contains information for the manuscript

sifFeaturesFinder-

Finds significant features shared between the LEFSe, rna seq and metagenome seq outputs of microbiome analyst. Must covert excel files to .txt files and change file paths in code

snakeMakePipeline

sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool