beiko-lab Goto Github PK

2020-bioinformaticsalgorithms

Tutorial assignments for CSCI4181/CSCI6802 (2020 edition)

amrtime

Tool to predict the presence of antimicrobial resistance in clinical metagenomes

ananke

Ananke: Clustering marker gene data by time-series patterns

ananke-docs

Beautiful static documentation for your API

ananke-ui

Shiny-based interface for exploring Ananke results.

arete

AMR/VF LGT focused bacterial genomics analysis workflow

arete-page

Static website for ARETE project information

beikome-r-ppt

A presentation for beikome lab.

cbw2021_module2_16s_analysis

cbwmeta2015

Support files for Canadian Bioinformatics Workshop, Metagenomics session 2015

csci4180_6801_2019

Scripts and data for 2019's CSCI4180 and CSCI6801 class.

dna_encoders

efaecium-niche

Code for reproducing e. faecium niche paper results.

evolccm

R package for CCM (Community Coevolution Model)

expositor

gene_neighborhoods_pipeline

A software pipeline to simplify the analysis and visualization of gene neighborhoods.

gengis

GenGIS (pronounced 'Genghis' like Genghis Khan) is a bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.

indizio

A visual analytics tool to investigate correlated data structures using heatmaps, networks, and network statistics.

megasat

High-throughput analysis of targeted microsatellite sequences.

mimb_16s

Repository containing scripts and files for 16S gene community analysis chapter in Methods in Molecular Biology

mockrobiota

A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.

pagel_implementation

pmerge

q2-ebd

A QIIME2 wrapper for the ExpressBetaDiversity program: https://github.com/dparks1134/ExpressBetaDiversity

q2-extractor

A small utility that maintains functions to pry data out of QIIME artifact and visualization files and transform as needed.

quorem_geno-mic

QUOREM: Query, Unify, and Organize Research on the Ecology of Microorganisms

rad

RAD reports from the Beiko lab students

radproc

sarand

To extract AMR genes and their neighborhood

sarandv0