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amniotic_fluid_tools

Scripts to help wrangle amniotic fluid metabolomic and metagenomic data

babs_db

bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

ihcp-diabetes

Peribank extraction and statistical analaysis of the association of diabetes and its treatment with cholestasis of pregnancy

kraken-biom

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

market_tracking

API tools for stock and index tracking/market analysis

medication_name_cleaner

Takes medication lists cleans up and standardizes with spelling matches against standard DB using fuzzywuzzy etc.

metaboliteid-translators

Builds a master list of metabolites and translates between metabolite ID types for different metabolic data sets in order to perform pathway analysis

metabolomicsplots

This repository contains the code that was used to create Hive and PLSDA plots for a metabolomic analysis of high fat diet.

metformin_peribank

This repository searches an entire database for all instances and versions of either metformin or insulin to classify subjects and outcomes in pregnancy.

poole

The Jekyll Butler. A no frills responsive Jekyll blog theme.

ppax

Supplementary media repository for the Prevention of Preterm Birth with Xylitol (PPaX Trial)

ppax-periodontal-data

Scripts to quanify periodontal metrics for PPaX in response to review

sequence_parsing

Small suite of tools for editing/parsing/demultiplexing DNA sequencing files (FASTQ etc).

shortbredcombine

Combine BioBakery ShortBred reports and summarize by group

vbac

Data extraction for VBAC study from peribank Database