Projects in Awesome Lists tagged with bacterial-genome-analysis

https://github.com/npavlovikj/prokevo

ProkEvo - an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.

bacterial-genome-analysis high-performance-computing high-throughput-computing osg pegasus-workflow-management

Last synced: 14 Oct 2024

https://github.com/danderson123/amira

A tool to detect acquired AMR genes directly from long read sequencing data.

amr assembly bacteria bacterial-genome-analysis epidemiology genotyping graph

Last synced: 16 Nov 2024

https://github.com/notthestallion/computer-vision-in-the-service-of-bacteriology

Computer vision in the service of bacteriology refers to the use of computer algorithms and technology to analyze and interpret images of bacteria for the purpose of identifying and characterizing different types of bacteria.

bacteria bacterial bacterial-database bacterial-genome-analysis bacterial-genomes bash computer-vision learning opencv

Last synced: 13 Nov 2024

https://github.com/gauravcodepro/ko-phylogenomics

analyzing bacterial genome based ontologies and phylogenomics informativeness

bacterial-genome-analysis bacterial-genomes geneontology genome-annotation ontologies ontology plant plantgenomes

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/ontology-annotation-count

a function to calculate the genome annotation for the microbiome and also for the other genomes. It will take a genome annotation or a text file and will prepare the count and also for the gene ontology analysis

bacterial-genome-analysis bacterial-genomes genome genome-analysis genome-annotation genome-sequencing microbiome microbiome-analysis plantgenomes plantgenomics

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/domain-analyzer

This repository contains a datascience based faster implementation of the domain predictions from the interpro scan and it will give you a complete domains information, coordinates and other associative information. I used a mapping dataframe approach to make it faster rather than looping it over and over.

bacterial-genome-analysis bacterial-genomes domains functional-programming functionaldomains fungal-genomes fungaleffectors interproscan plantgenomes protein-sequence protein-structure proteindomains

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/evolutionary-rate-analyer

A R function for the analysis of the evolutionary rates from the fasta files, and uses the ka/ks and the dn/ds and plots the evolutionary rates.

bacterial-genome-analysis bacterial-genomes bioinformatics evolution evolutionary-computation fungal-genomes fungal-metagenomics plantgenomics rprogramming

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/bacterial-keras

A keras implementation of machine learning for bacterial genomes, takes a fasta file and the annotation features and the genes you want to train the keras model

bacterial-genome-analysis bacterial-genomes keras machinelearning

Last synced: 09 Nov 2024

https://github.com/applicativesystem/go-metagenome-placer

metegnome sequence extractions from MAGs

bacterial-genome-analysis bacterial-genomes metagenomes metagenomics metagenomics-data metagenomics-toolkit

Last synced: 16 Dec 2024

https://github.com/applicativesystem/bacterial-insertion-element

string based approach to check for the instertion element in bacterial genomes

bacterial-genome-analysis bacterial-genome-sequence bacterial-genomes genome-analysis insertion-elements metagenomes

Last synced: 16 Dec 2024

https://github.com/applicativesystem/domain-analyzer

domain analyzer for analyzing interpro domains

bacterial-domains bacterial-genome-analysis bacterial-genomes bioinfromatics domain-analysis genome-analysis interpro

Last synced: 16 Dec 2024

https://github.com/applicativesystem/bacterial-metagenomes

bacterial mategnomes assembly and pangenomes

bacterial-genome-analysis bacterial-genomes bioinformatics metagenomics metagenomics-data pangenome

Last synced: 16 Dec 2024

https://github.com/gauravcodepro/domain-graphs

interpro to graphs for analyzing domains.

annotation-tool bacterial-genome-analysis bacterialmetagenomics directed-acyclic-graph directed-graphs fungal-metagenomics graph-algorithms interproscan protein-protein-interaction proteindomains

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/trinity-blast-machine-learning

a scalable and faster implementation for the genome and the transcriptome annotations for large scale sequencing datasets.

bacterial-genome-analysis bacterial-genomes genome-annotation genome-assembly plantgenomes plantgenomics transcriptome-annotation transcriptome-assembly transcriptome-profiling-data transcriptome-wide transcriptomics trinity

Last synced: 09 Nov 2024

https://github.com/gauravcodepro/pangenomemetagenomicsnormalizer

a pangenome metagenomics normalizer, given a gene ontology based presence and absence and a species file, it first summarizes the count across the species and then takes the count of the gene ontologies and present a ratio The higher the ratio the more presence of that ontology across the species.

bacterial-genome-analysis bacterialmetagenomics bioinformatics fungal-metagenomics metagenomics metagenomics-counts pangenomics

Last synced: 09 Nov 2024