rajaldebnath

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).

animate.phyloseq

Animation addon tool for phyloseq package

co-occurrence

R scripts for performing co-occurrence analyses

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/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/

rajaldebnath/ANCOM

R scripts for Analysis of Composition of Microbiomes (ANCOM).

rajaldebnath/awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

rajaldebnath/bcbb

Incubator for useful bioinformatics code, primarily in Python and R

rajaldebnath/bioicons

A library of free open source icons for science illustrations in biology and chemistry

rajaldebnath/biomagician

Useful tools in microbiomics and metagenomics

rajaldebnath/CAFE5

Version 5 of the CAFE phylogenetics software

rajaldebnath/funannotate

Eukaryotic Genome Annotation Pipeline

rajaldebnath/GAAS

Genome Assembly and Annotation Service code

rajaldebnath/genome-scripts

Genome Scripts used in fungal comparative genomics

rajaldebnath/GenomeAnnotation

Various scripts that I have created that are useful for genome annotation (repeats & proteins)

rajaldebnath/ggcoverage

Visualize and annotate genomic coverage with ggplot2

rajaldebnath/gggenomes

A grammar of graphics for comparative genomics

rajaldebnath/ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics

rajaldebnath/gmap

An R package to visualize genetic maps.

rajaldebnath/juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

rajaldebnath/KEGGCharter

A tool for representing genomic potential and transcriptomic expression into KEGG pathways

rajaldebnath/lastz

Program for aligning DNA sequences, a pairwise aligner.

rajaldebnath/learning_vcf_file

Learning the Variant Call Format

rajaldebnath/mummer2circos

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

rajaldebnath/profile_dists

Profile Dists: Convenient package for comparing genetic similarity of samples based on allelic profiles

rajaldebnath/rajaldebnath.github.io

rajaldebnath/reCOGnizer

A tool for domain based annotation with databases from the Conserved Domains Database

rajaldebnath/rnabio.org

website for the rnaseq course

rajaldebnath/Roary

Rapid large-scale prokaryote pan genome analysis

rajaldebnath/svim

Structural Variant Identification Method using Long Reads

rajaldebnath/tidyverse_approach

materials for R workshop series, revised to emphasize tidyverse packages

rajaldebnath/treedata-book

:books: a complete reference book for treeio, tidytree and ggtree packages

rajaldebnath/trimal

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

rajaldebnath/wttr.in

:partly_sunny: The right way to check the weather