Pinned Repositories
MIB20306MicrobialPhysiology
Teaching MIB20306: Interactive app created to teach proteomics guided investigation of bacterial metabolism. We use Intestinimonas butyriciproducens as example.
microbiome
microbiome R package
chkMocks
Check your mock communities from microbiome sequencing experiments
dysbiosisR
The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures
Indian-gut-microbiota
Data and analysis code for the Indian gut microbiota study
Microbial-bioinformatics-introductory-course-Material-2018
microbiomeutilities
The is mostly a wrapper tool using phyloseq and microbiome R packages.
microbiomeutilities-shiny
Try it out- Want to develop this as a teaching tool to demonstrate commonly done microbial diversity analysis methods/concepts
syncomR
R package with wrapped functions for synthetic microbial community analysis.
Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
microsud's Repositories
microsud/Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
microsud/microbiomeutilities
The is mostly a wrapper tool using phyloseq and microbiome R packages.
microsud/dysbiosisR
The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures
microsud/syncomR
R package with wrapped functions for synthetic microbial community analysis.
microsud/chkMocks
Check your mock communities from microbiome sequencing experiments
microsud/Bacterial-Proteomics-in-R
microsud/Db-MM-10
Synthetic gut minimal microbiome with 10-core species
microsud/Microbial-bioinformatics-introductory-course-Material-2018
microsud/BigDataBasicInsights
microsud/biomeomics
rivm toolbox
microsud/CoronaWatchNL
COVID-19 disease count cases in The Netherlands by RIVM, LCPS and NICE
microsud/datasharing
The Leek group guide to data sharing
microsud/gutmicrobe_webpage.io
microsud/ili_elderly_microbiota
microsud/jeevanuDB
Example data sets and other data type for microbiome package https://github.com/microbiome/microbiome
microsud/MDb-MM
microsud/metagenomic_binning_review
Code used to analyse and plot metadata of metagenomic binning tools
microsud/MIB20306MicrobialPhysiology
Teaching MIB20306: Interactive app created to teach proteomics guided investigation of bacterial metabolism. We use Intestinimonas butyriciproducens as example.
microsud/microbiomedatarepo
Access to few of the publicly available gut microbiome data sets as part of the microbiomeutilities R package
microsud/microbiomeDataSets
Experiment Hub based microbiome datasets
microsud/microsud
microsud/mni-website
microsud/pepper
PePPer - Personalized Perturbation Profiler
microsud/quarto_microbiome
microsud/R_for_Microbial_Ecology
Main webpage with information, tutorial, etc
microsud/Shetty_et_al_Anaerobutyricum_physiology
Codes from study on characterization of physiology of Anaerobutyricum and related species
microsud/sudarshanshetty.io
Personal Website
microsud/TeachingMIB20306
Teaching MIB20306: Interactive app created to teach proteomics guided investigation of bacterial metabolism. We use Intestinimonas butyriciproducens as example.
microsud/testFieldOpenScienceMicrobiome
microsud/urt_microbiota