Sudarshan's Projects
Example data sets and other data type for microbiome package https://github.com/microbiome/microbiome
A series of scripts for annotating KEGG reads from metagenomic data and visualizing the output.
[R package]: questionnaires scoring
A metagenomic analysis pipeline
Metatranscriptomics Tutorial
Teaching MIB20306: Interactive app created to teach proteomics guided investigation of bacterial metabolism. We use Intestinimonas butyriciproducens as example.
Set of useful functions and scripts for analyzing amplicon Miseq data.
Access to few of the publicly available gut microbiome data sets as part of the microbiomeutilities R package
Experiment Hub based microbiome datasets
A Rmarkdown template for microbial community analysis.
This website gives an introduction to microbial community analysis.
The is mostly a wrapper tool using phyloseq and microbiome R packages.
Try it out- Want to develop this as a teaching tool to demonstrate commonly done microbial diversity analysis methods/concepts
An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles
Record of analysis for peat microbiome manuscript
PePPer - Personalized Perturbation Profiler
Mapping for 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:
simple proteomic assistant
Qiita - A multi-omics databasing effort
Main webpage with information, tutorial, etc
Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
A repository for setting up a RNAseq workflow
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