Taojun Wang's repositories
2018-cicese-metatranscriptomics
repo for cicese metatranscriptomics workshop, nov 2018
biom-format
The Biological Observation Matrix (BIOM) Format Project
CC-Linear-mixed-models
Introduction to linear mixed models
Comparative_Genomics
Micro 612 genomics workshop
daphne_ecoli-diauxie
Emergent sub-population behavior uncovered with a community dynamic metabolic model of Escherichia coli diauxic growth
Gavriilidou_et_al_Flavos_ComparativeGenomics
This repository contains the codes and files for reproducing the results presented in the respective publication. Raw reads and sequences have been deposited in ENA under accession number PRJEB35092.
Microbial-bioinformatics-introductory-course-Material-2018
Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL
microbiomeMarker
R package for microbiome biomarker discovery
microbiomeSeq
An R package for microbial community analysis in an environmental context
NG-Tax
NG-Tax is an improved pipeline for 16S rRNA gene amplicon sequencing data. Several novel steps ensure improved robustness against errors associated with technical aspects of these studies, such as PCR protocols, choice of 16S rRNA gene variable region and variable rates of sequencing error. The commonly reported problems such as many un- or poorly classified OTUs, inflated richness and diversity, taxonomic profiles that do not match the expected ones, region dependent taxonomic classification and results being highly dependent on minor changes in the experimental setup have been tackled with NG-Tax.
samsa2
SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
Tools-Microbiome-Analysis
A list of R environment based tools for marker gene microbiome data exploration, statistical analysis and visualization