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/16S
Notes and scripts for 16S microbiome analysis
rajaldebnath/Bash-Oneliner
A collection of handy Bash One-Liners and terminal tricks for data processing and Linux system maintenance.
rajaldebnath/BinSanity
Unsupervised Clustering of Environmental Microbial Assemblies Using Coverage and Affinity Propagation
rajaldebnath/Bio-py
Some useful python scripts for biologists
rajaldebnath/bioscripts
some useful scripts for working with genomics and sequencing data
rajaldebnath/broCode
self made scripts
rajaldebnath/CAFE
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
rajaldebnath/CONCOCT
Clustering cONtigs with COverage and ComposiTion
rajaldebnath/DGE_workshop_salmon
rajaldebnath/ELB18S
ELB18S - Entry Level Bioinformatics (Second course in 2018)
rajaldebnath/FastANI
Fast Whole-Genome Similarity (ANI) Estimation
rajaldebnath/Fastaq
Python3 scripts to manipulate FASTA and FASTQ files
rajaldebnath/GMATA
software GMATA
rajaldebnath/grabseqs
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
rajaldebnath/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
rajaldebnath/kaiju
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
rajaldebnath/KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
rajaldebnath/METABOLIC
A scalable high-throughput metabolic and biogeochemical functional trait profiler
rajaldebnath/microbiomeSeq
An R package for microbial community analysis in an environmental context
rajaldebnath/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
rajaldebnath/NCBImeta
Efficient and comprehensive metadata acquisition from the NCBI databases (includes SRA).
rajaldebnath/oneliners
Useful bash one-liners for bioinformatics.
rajaldebnath/radiator
RADseq Data Exploration, Manipulation and Visualization using R
rajaldebnath/resume
My resume
rajaldebnath/RNA-seq-analysis
RNAseq analysis notes from Ming Tang
rajaldebnath/seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
rajaldebnath/seqtk
Toolkit for processing sequences in FASTA/Q formats
rajaldebnath/shinyCircos
an R/shiny application for creation of Circos plot interactively
rajaldebnath/Singularity-Tutorial
How to use Singularity!
rajaldebnath/sv-cnv-studies
:books: Relevant papers for CNV and SV approaches