Pinned Repositories
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
arete
AMR/VF LGT focused bacterial genomics analysis workflow
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.
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
RADProc
sarand
To extract AMR genes and their neighborhood
sarand_fullVersion
To extract AMR genes and their neighborhood
Dr. Beiko's Lab's Repositories
beiko-lab/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.
beiko-lab/mimb_16S
Repository containing scripts and files for 16S gene community analysis chapter in Methods in Molecular Biology
beiko-lab/arete
AMR/VF LGT focused bacterial genomics analysis workflow
beiko-lab/ananke
Ananke: Clustering marker gene data by time-series patterns
beiko-lab/AMRtime
Tool to predict the presence of antimicrobial resistance in clinical metagenomes
beiko-lab/MEGASAT
High-throughput analysis of targeted microsatellite sequences.
beiko-lab/RADProc
beiko-lab/sarand
To extract AMR genes and their neighborhood
beiko-lab/sarand_fullVersion
To extract AMR genes and their neighborhood
beiko-lab/2020-BioinformaticsAlgorithms
Tutorial assignments for CSCI4181/CSCI6802 (2020 edition)
beiko-lab/CBW2021_Module2_16S_Analysis
beiko-lab/ananke-ui
Shiny-based interface for exploring Ananke results.
beiko-lab/DNA_encoders
beiko-lab/q2-extractor
A small utility that maintains functions to pry data out of QIIME artifact and visualization files and transform as needed.
beiko-lab/QUOREM_geno-MIC
QUOREM: Query, Unify, and Organize Research on the Ecology of Microorganisms
beiko-lab/ARETE-page
Static website for ARETE project information
beiko-lab/Expositor
beiko-lab/Indizio
A visual analytics tool to investigate correlated data structures using heatmaps, networks, and network statistics.
beiko-lab/RAD
RAD reports from the Beiko lab students
beiko-lab/ananke-docs
Beautiful static documentation for your API
beiko-lab/CSCI4180_6801_2019
Scripts and data for 2019's CSCI4180 and CSCI6801 class.
beiko-lab/efaecium-niche
Code for reproducing e. faecium niche paper results.
beiko-lab/evolCCM
R package for CCM (Community Coevolution Model)
beiko-lab/gene_neighborhoods_pipeline
A software pipeline to simplify the analysis and visualization of gene neighborhoods.
beiko-lab/mockrobiota
A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.
beiko-lab/Pagel_Implementation
beiko-lab/PMERGE
beiko-lab/q2-ebd
A QIIME2 wrapper for the ExpressBetaDiversity program: https://github.com/dparks1134/ExpressBetaDiversity
beiko-lab/sarandV0
beiko-lab/training_resources
Collation of useful training materials