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/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/2017-ncbi-taxdump
rajaldebnath/alignment-and-variant-calling-tutorial
basic walk-throughs for alignment and variant calling from NGS sequencing data
rajaldebnath/anvio
An analysis and visualization platform for 'omics data
rajaldebnath/awesome-public-datasets
An awesome list of high-quality open datasets in public domains (on-going). By everyone, for everyone!
rajaldebnath/bac-genomics-scripts
Collection of scripts for bacterial genomics
rajaldebnath/bedtools2
A powerful toolset for genome arithmetic.
rajaldebnath/Easyfig
Development version of Easyfig
rajaldebnath/epp622
UTK Bioinformatics Applications
rajaldebnath/F1000_workflow
rajaldebnath/FastQC
rajaldebnath/illumina-utils
A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
rajaldebnath/megahit
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
rajaldebnath/Metagenome
rajaldebnath/metagenomics-workshop
Metagenomics Workshop
rajaldebnath/microbiome
microbiome R package
rajaldebnath/microbiome_helper
An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools.
rajaldebnath/ncbi_blast_tutorial
Short introduction to command line NCBI blast tools
rajaldebnath/PAML
This is code for running Orthofinder -> PAML
rajaldebnath/PanViz
D3 based visualisation for comparative genomics
rajaldebnath/PAPER_LeeSorensen_ISMEJ_2017
Workflows and R scripts for Lee and Sorensen et al
rajaldebnath/PEAR
Pair-End AssembeR
rajaldebnath/reads-for-assembly
Simulate metagenomic short reads from one or more populations.
rajaldebnath/rnaseq_tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
rajaldebnath/sortmerna
SortMeRNA: a sequence analysis tool for filtering, mapping and clustering NGS reads.
rajaldebnath/SUPER-FOCUS
A tool for agile functional analysis of shotgun metagenomic data
rajaldebnath/trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly
rajaldebnath/uniprot
retrieve protein sequence identifiers and metadata from http://uniprot.org
rajaldebnath/vsearch
Versatile open-source tool for metagenomics
rajaldebnath/workshop
Genome sequence comparison workshop