knights-lab Goto Github PK

adonc

Make a Python module into an executable - (pronounced eggsecutable)

akronymer

Ultrafast genome- and dataset-scale distance matrix and phylogenetic tree creation

analysis_italy

analysis_shogun

Analysis scripts and code for reproducing the analysis for the SHOGUN paper

analysis_tree

arthritis_analysis

Code for the analysis of the IBD and arthritis data

autoqiime

Picks OTUs using NINJA-OPS then runs standard QIIME pipeline

betadiv

Materials and analyses for "Microbiome beta diversity analyses and visualization." A discussion of beta diversity analysis methods, factors we must consider in each step, and how we might better use these methods in forthcoming microbiome research.

bugbase

bugbrowser

burst

An ultrafast optimal aligner for mapping large NGS data to large genome databases.

climate-trace-shipping

conda-recipes

Conda recipes for the knights lab

dietstudy

Diet Study

dietstudy_analyses

dojo

douc_gut_sites

Microbiome of red-shanked douc gut sites

ermin-standards

Emissions Report Minimum INformation (ERMIN) Standards

food_tree

USDA Nutrition codes Tree

foodworks

Experimenting with Bayesian Networks for predicting day-to-day microbiome fluctuations

garlicmustard

general-mills-tufts-analyses

helix

Short scripts for use within the knights-lab

ibs-timeseries

imp-open-ref

Open Ref BURST with IMP data

imp_analyses

immigrant microbiome project related analyses

kafan

Lossless data compression codec specialized for sequence data

kernel-methods

knights-lab.github.io

Knights Lab website via Github pages

lmdist

LMdist is an unsupervised algorithm for correcting oversaturated pairwise distance and dissimilarity measures. Compatible with any pairwise beta diversity measure, LMdist will uncover underlying environmental gradients and resolve arches/horseshoes in ordination.