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/

ANCOM

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

awesome-genome-visualization

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

bcbb

Incubator for useful bioinformatics code, primarily in Python and R

bioicons

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

biomagician

Useful tools in microbiomics and metagenomics

CAFE5

Version 5 of the CAFE phylogenetics software

Code-documentation

Project code documentation

funannotate

Eukaryotic Genome Annotation Pipeline

GAAS

Genome Assembly and Annotation Service code

genome-scripts

Genome Scripts used in fungal comparative genomics

GenomeAnnotation

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

ggcoverage

Visualize and annotate genomic coverage with ggplot2

gggenomes

A grammar of graphics for comparative genomics

ggkegg

Analyzing and visualizing KEGG information using the grammar of graphics

gmap

An R package to visualize genetic maps.

juicer

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

KEGGCharter

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

lastz

Program for aligning DNA sequences, a pairwise aligner.

learning_vcf_file

Learning the Variant Call Format

METABOLIC

A scalable high-throughput metabolic and biogeochemical functional trait profiler

mummer2circos

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

profile_dists

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

rajaldebnath.github.io

reCOGnizer

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

Roary

Rapid large-scale prokaryote pan genome analysis

tidyverse_approach

materials for R workshop series, revised to emphasize tidyverse packages

treedata-book

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

trimal

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

wttr.in

:partly_sunny: The right way to check the weather