AhmedElsherbini

ggplot2

An implementation of the Grammar of Graphics in R

bash-handbook

:book: For those who wanna learn Bash

ggstatsplot

Enhancing {ggplot2} plots with statistical analysis 📊📣

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

MolecularNodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

gggenes

➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

biocode

Bioinformatics code libraries and scripts

abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

ggsankey

Make sankey, alluvial and sankey bump plots in ggplot

PPanGGOLiN

Build a partitioned pangenome graph from microbial genomes

NatParksPalettes

Color palette package inspired by National Parks

treemapify

🌳 Draw treemaps in ggplot2

mlst

:id: Scan contig files against PubMLST typing schemes

carveme

CarveMe: genome-scale metabolic model reconstruction

run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

dragonflye

:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads

perfect-bioinformatic-tools

What should perfect bioinformatic tools be like?

funcscan

(Meta-)genome screening for functional and natural product gene sequences

cytoscape_tutorials

A set of Cytoscape tutorials for my students

MetaCerberus

Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data

speciesprimer

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.

public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.

mobilome-annotation-pipeline

tax_myPHAGE

Workflow to assign Taxonomy to a bacteriophage genome isolate

synthaser

Parse NCBI CD-search results to find and visualise the domain architecture of secondary metabolite synthases

fastq-info

Calculate fastq reads and sequencing coverage

phammseqs

Assort phage protein sequences into phamilies using MMseqs2

phamclust

Pham-based genome clustering