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/annovarR
annovarR: a variant annotation and visualization system based on R and Shiny framework
rajaldebnath/blobtools
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
rajaldebnath/CoDa_microbiome_tutorial
Workshop for NGS'18 conference, Barcelona 2018
rajaldebnath/COG
Scripts and steps for making a consolidated COG database file for tools like DIAMOND.
rajaldebnath/CoNetinR
Implementation of CoNet in R
rajaldebnath/decontam-1
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
rajaldebnath/DESeq2
Differential gene expression analysis based on the negative binomial distribution
rajaldebnath/diamond
Accelerated BLAST compatible local sequence aligner.
rajaldebnath/factoextra
Extract and Visualize the Results of Multivariate Data Analyses
rajaldebnath/genomescope
Fast genome analysis from unassembled short reads
rajaldebnath/intro-to-r
Scripts and data to go along with introductions to R
rajaldebnath/IRanges
Infrastructure for manipulating intervals on sequences
rajaldebnath/metacoder
Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
rajaldebnath/MetagenomicAntibioticResistance
NastyBugs: a simple method for extracting antimicrobial resistance information from metagenomes
rajaldebnath/Microbiome-Analysis-Using-R
Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.
rajaldebnath/mirna
microRNA profiling pipeline
rajaldebnath/NetworkUtils
Utility functions for microbial network analysis
rajaldebnath/pgap
NCBI Prokaryotic Genome Annotation Pipeline
rajaldebnath/pheatmap
Pretty heatmaps
rajaldebnath/rentrez
talk with NCBI entrez using R
rajaldebnath/SCNIC
Sparse Cooccurence Network Investigation for Compositional data
rajaldebnath/spades
SPAdes Genome Assembler
rajaldebnath/Synima
Synteny Imager
rajaldebnath/taxadiva
TAXonomy Assignment and DIVersity Assessment - wrapper script for facilitating analysis of nifH amplicon sequences
rajaldebnath/tutorials
Tutorials on phylogenetic and phylogenomic methods
rajaldebnath/tutorials-1
Tutorials on how to use the microGVL to do common bacterial bioinformatic tasks
rajaldebnath/tximport
Import and summarize transcript-level estimates for gene-level analysis
rajaldebnath/VariantAnnotation
Annotation of Genetic Variants
rajaldebnath/vcfR
Tools to work with variant call format files
rajaldebnath/workshop-popgenome
Tutorial about R package PopGenome