munamerchan Goto Github PK

00_pangenome_analysis

Pangenome Analysis Workflow with Prodigal and CD-HIT

2021_bioinformatics_fellowship

Project 2 Resources

aaftf

Automatic Assembly For The Fungi

abricate

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

amazonmicrobiomedynamics

amptk

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

anvio

An analysis and visualization platform for 'omics data

asap

A scalable bacterial genome assembly, annotation and analysis pipeline

awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

awesome-genome-visualization

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

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

bac-genomics-scripts

Collection of scripts for bacterial genomics

bacterial-genomics

Course materials for "Working with Bacterial Genomes"

bactopia

A flexible pipeline for complete analysis of bacterial genomes

be_iss_pangenomes

Data repo for our publication, "Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil. mSystems 4:e00281-18."

biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

bioconda-recipes

Conda recipes for the bioconda channel.

biodata

All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")

bioinformatics-training-collection

A collection of resources for learning about tools and programming languages related to Bioinformatics

bioinftraining

Repository for bioinformatics training at the Norwegian Veterinary Institute

biomartr

Genomic Data Retrieval with R

cancer_wgs_scripts

Re-analysis of data provided by Gihawi et al. 2023 bioRxiv

candida_auris_cladevi

WGS analysis for Candida auris

cayman

cbbp-transcriptomics

cgrphylo

CGR package for phylogeny. Pipeline compare multiple whole genome sequences using alignment free approach Chaos Game Representation (CGR). CRG core function creates the frequencies object for each sequence which can be used to calculate distances among sequences.

childhood_micro_metaanalysis

Code for analysis of multiple childhood gut microbiome datasets

cogclassifier

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

comparative_genomics

Toolbox for comparative genomics

corestats

These materials support the Core statistics sessions, run through the Bioinformatics Training Facility at the University of Cambridge.