rajaldebnath
Microbial ecology | Microbiology | Bioinformatics https://scholar.google.com/citations?user=hiB40poAAAAJ&hl=en
Central Silk BoardIndia
Pinned Repositories
16S
Notes and scripts for 16S microbiome analysis
16S-rDNA-V3-V4
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
2016-01-18-MSU
Course Page for 1 day Data Carpentry @ MSU
2017-ncbi-taxdump
alignment-and-variant-calling-tutorial
basic walk-throughs for alignment and variant calling from NGS sequencing data
AMPHORA2
An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
ANCOM
R scripts for Analysis of Composition of Microbiomes (ANCOM).
co-occurrence
R scripts for performing co-occurrence analyses
pyani
Application and Python module for average nucleotide identity analyses of microbes.
RNASeq_Trinity_Tuxedo_Workshop
materials for the RNA-Seq workshop on Trinity and Tuxedo, covering de novo and genome-guided transcript assembly and downstream analysis.
rajaldebnath's Repositories
rajaldebnath/co-occurrence
R scripts for performing co-occurrence analyses
rajaldebnath/2016-01-18-MSU
Course Page for 1 day Data Carpentry @ MSU
rajaldebnath/AMPHORA2
An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
rajaldebnath/animate.phyloseq
Animation addon tool for phyloseq package
rajaldebnath/bacterial_GWAS_tutorial
Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop
rajaldebnath/biom
Development version of the biom package for R
rajaldebnath/BRIG
BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
rajaldebnath/classifier
RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
rajaldebnath/dada2
Fast, accurate, single-nucleotide resolution for amplicon data. INSTALLATION INSTRUCTIONS AND TUTORIAL ON THE FRONT PAGE:
rajaldebnath/decontam
rajaldebnath/Edwards-et-al.-2014
rajaldebnath/ggdendro
Tools to extract dendrogram plot data for use with ggplot
rajaldebnath/ggplot2
An implementation of the Grammar of Graphics in R
rajaldebnath/matR
Metagenomics Analysis Tools
rajaldebnath/MG-RAST-Tools
Repository of script tools, examples, and contributed code for using the MG-RAST API
rajaldebnath/microbeco2015
rajaldebnath/microbial-informatics-2014
Microbial Whole Genome Sequence data analysis labs for 2014
rajaldebnath/orthomcl
Fork of orthomcl 2.0, (http://www.orthomcl.org)
rajaldebnath/pangenome
Models of the Microbial Pangenome
rajaldebnath/Pathway-Analysis-Tutorial
rajaldebnath/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:
rajaldebnath/phyloseq-extensions
Extensions for the phyloseq package for R
rajaldebnath/qiime
Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests
rajaldebnath/qiime.io
Experimental support for loading and interacting with QIIME files in R.
rajaldebnath/RASTtk-Distribution
KBase distribution module for RASTtk.
rajaldebnath/RDPTools
Collection of commonly used RDP Tools for easy building
rajaldebnath/statistical-analysis-python-tutorial
Statistical Data Analysis in Python