microsud/Tools-Microbiome-Analysis

A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

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microsud/microbiomeutilities

The is mostly a wrapper tool using phyloseq and microbiome R packages.

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microsud/westernization Fork of jsescobar/westernization

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microsud/urt_microbiota

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microsud/TutorialsMicrobiomeAnalysis.github.io 📦

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microsud/tufterhandout Fork of sachsmc/tufterhandout

Output formats for Tufte-style handouts in pdf and html for Rmarkdown

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microsud/tufte Fork of rstudio/tufte

Tufte Styles for R Markdown Documents

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microsud/TeachingMIB20306

Teaching MIB20306: Interactive app created to teach proteomics guided investigation of bacterial metabolism. We use Intestinimonas butyriciproducens as example.

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microsud/testFieldOpenScienceMicrobiome

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microsud/syncomR

R package with wrapped functions for synthetic microbial community analysis.

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microsud/SARTools Fork of PF2-pasteur-fr/SARTools

Statistical Analysis of RNA-Seq Tools

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microsud/Shetty_et_al_Anaerobutyricum_physiology Fork of mibwurrepo/Shetty_et_al_Anaerobutyricum_physiology

Codes from study on characterization of physiology of Anaerobutyricum and related species

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microsud/sudarshanshetty.io

Personal Website

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microsud/R_for_Microbial_Ecology Fork of mibwurrepo/R_for_Microbial_Ecology

Main webpage with information, tutorial, etc

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microsud/RforProteomics Fork of lgatto/RforProteomics

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

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microsud/RNAseq-workflow Fork of twbattaglia/RNAseq-workflow

A repository for setting up a RNAseq workflow

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microsud/quarto_microbiome

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microsud/qiita Fork of qiita-spots/qiita

Qiita - A multi-omics databasing effort

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microsud/preoteoassistant

simple proteomic assistant

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microsud/phyloseq Fork of joey711/phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

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microsud/phylogeo Fork of zachcp/phylogeo

Mapping for Phyloseq

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microsud/pepper Fork of emreg00/pepper

PePPer - Personalized Perturbation Profiler

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microsud/peat-microbiome Fork of davidelliott/peat-microbiome

Record of analysis for peat microbiome manuscript

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microsud/omixer-rpmR Fork of omixer/omixer-rpmR

An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles

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microsud/mni-website

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microsud/microbiomeutilities-shiny

Try it out- Want to develop this as a teaching tool to demonstrate commonly done microbial diversity analysis methods/concepts

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microsud/microsud

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microsud/MicrobiomeX2 Fork of TBrach/MicrobiomeX2

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microsud/microbiometutorials.gihub.io

This website gives an introduction to microbial community analysis.

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microsud/microbiometemplate

A Rmarkdown template for microbial community analysis.

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microsud/microbiomeDataSets Fork of microbiome/microbiomeDataSets

Experiment Hub based microbiome datasets

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microsud/microbiomedatarepo

Access to few of the publicly available gut microbiome data sets as part of the microbiomeutilities R package

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microsud/Microbial-bioinformatics-introductory-course-Material-2018 Fork of mibwurrepo/Microbial-bioinformatics-introductory-course-Material-2018

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microsud/MicrobeMiseq Fork of DenefLab/MicrobeMiseq

Set of useful functions and scripts for analyzing amplicon Miseq data.

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microsud/MIB20306MicrobialPhysiology Fork of mibwurrepo/MIB20306MicrobialPhysiology

Teaching MIB20306: Interactive app created to teach proteomics guided investigation of bacterial metabolism. We use Intestinimonas butyriciproducens as example.

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microsud/Metatranscriptome-Workshop Fork of ParkinsonLab/Metatranscriptome-Workshop

Metatranscriptomics Tutorial

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microsud/MDb-MM

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microsud/MAP Fork of alesssia/MAP

A metagenomic analysis pipeline

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microsud/lbscorer Fork of lbraglia/lbscorer

[R package]: questionnaires scoring

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microsud/kegg-r-ator Fork of marubel/kegg-r-ator

A series of scripts for annotating KEGG reads from metagenomic data and visualizing the output.

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microsud/Kamneva_2016 Fork of olgakamneva/Kamneva_2016

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microsud/jeevanuDB

Example data sets and other data type for microbiome package https://github.com/microbiome/microbiome

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microsud/Intestinal-Microbiome-Western-Adults

Files and codes used for analysis of data reported in the review by Shetty et al. 2016.

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microsud/ink Fork of thinker3197/ink

A jekyll theme for humans

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microsud/Indian-gut-microbiota

Data and analysis code for the Indian gut microbiota study

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microsud/ili_elderly_microbiota

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microsud/gutmicrobe_webpage.io

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microsud/Gut-microbiota-Celiac-disease

R scripts used for analysis of data reported in Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Patients with Celiac Disease and Controls

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microsud/gLVInterNetworks Fork of lkshrsch/gLVInterNetworks

Inference of interaction networks from time series data fitting a generalized Lotka Volterra model

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microsud/Fantaxtic Fork of gmteunisse/fantaxtic

Fantaxtic plots for phyloseq objects!

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microsud/GEN-tools Fork of masgra/GEN-tools

Testing different Ecolocical Network Interference tools on metatranscriptomic data

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microsud/flexdashboard Fork of rstudio/flexdashboard

Easy interactive dashboards for R

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microsud/ecostates Fork of cascobayesian/ecostates

Infinite dimensional Dirichlet-multinomial mixtures for ecological count data

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microsud/EcologicalStabilityPropertiesComputation Fork of fcentler/EcologicalStabilityPropertiesComputation

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microsud/DirFactor Fork of boyuren158/DirFactor

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microsud/Db-MM-10

Synthetic gut minimal microbiome with 10-core species

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microsud/datasharing Fork of jtleek/datasharing

The Leek group guide to data sharing

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microsud/DataScienceR Fork of ujjwalkarn/DataScienceR

a curated list of R tutorials for Data Science, NLP and Machine Learning

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microsud/CoronaWatchNL Fork of J535D165/CoronaWatchNL

COVID-19 disease count cases in The Netherlands by RIVM, LCPS and NICE

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microsud/competitive_network Fork of StefanoAllesina/competitive_network

Code accompanying the manuscript "Higher-order interactions stabilize dynamics in a competitive network model"

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microsud/Comparison-of-Small-Gut-and-Whole-Gut-Microbiota-of-First-Degree-Relatives-with-Adult-Celiac-Disease Fork of rahulnccs/Comparison-of-Small-Gut-and-Whole-Gut-Microbiota-of-First-Degree-Relatives-with-Adult-Celiac-Disease

Comparative bacterial community analysis in Celiac disease patients and control subjects.

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microsud/biomeomics

rivm toolbox

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microsud/BEEM-static Fork of lch14forever/beem-static

BEEM-static: An R package for inferring microbial interactions based on Lotka-Volterra models

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microsud/BigDataBasicInsights

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microsud/bcbioRNASeq Fork of hbc/bcbioRNASeq

Quality control and differential expression for bcbio RNA-seq experiments.

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microsud/bayesplot Fork of stan-dev/bayesplot

bayesplot R package for plotting Bayesian models

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microsud/Baxter_FITs_Microbiome_2016 Fork of SchlossLab/Baxter_FITs_Microbiome_2016

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microsud/Bacterial-Proteomics-in-R

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microsud/Atashgahi-et-al.-XenobioticReview2018 Fork of mibwurrepo/Atashgahi-et-al.-XenobioticReview2018

Codes to reproduce figures from Atashgahi et al., XenobioticReview2018

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microsud/ANCOM Fork of FrederickHuangLin/ANCOM-Code-Archive

R scripts for Analysis of Composition of Microbiomes (ANCOM).

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microsud/chkMocks

Check your mock communities from microbiome sequencing experiments

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microsud/dysbiosisR

The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures

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