Projects in Awesome Lists tagged with microbiology

https://github.com/moshi4/pygenomeviz

A genome visualization python package for comparative genomics

bioinformatics comparative-genomics genbank genomics genomics-visualization gff gff3 matplotlib microbial-genomics microbiology python synteny visualization

Last synced: 15 May 2025

https://github.com/microbiome/microbiome

microbiome R package

hitchip hitchip-atlas human-microbiome microbiology microbiome microbiome-analysis phyloseq population-study r

Last synced: 16 May 2025

https://github.com/mrolm/drep

Rapid comparison and dereplication of genomes

assembly bioinformatics metagenomics microbial-genomes microbiology

Last synced: 15 May 2025

https://github.com/oschwengers/platon

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

assembly bacteria bioinformatics contigs microbiology ngs plasmids wgs

Last synced: 07 May 2025

https://github.com/msberends/amr

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.

amr antimicrobial-data epidemiology microbiology r software

Last synced: 16 May 2025

https://github.com/oschwengers/referenceseeker

Rapid determination of appropriate reference genomes.

ani bioinformatics mash microbiology reference-genomes refseq wgs

Last synced: 19 Dec 2024

https://github.com/aleimba/bac-genomics-scripts

Collection of scripts for bacterial genomics

annotation bioinformatics bioperl blast computational-biology genomics microbial-genomics microbiology mlst ngs opensource perl science scripts-collection sequencing unix

Last synced: 02 Apr 2025

https://github.com/dmnfarrell/teaching

scripts and notes for learning

bioinformatics bokeh jupyter microbiology python pyviz

Last synced: 15 Apr 2025

https://github.com/chasemc/IDBacApp

A MALDI Mass Spectrometry Bioinformatics Platform

mass-spectrometry microbiology r shiny

Last synced: 04 Dec 2024

https://github.com/chasemc/idbacapp

A MALDI Mass Spectrometry Bioinformatics Platform

mass-spectrometry microbiology r shiny

Last synced: 18 Mar 2025

https://github.com/jlumpe/gambit

A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.

bioinformatics genomics microbiology public-health whole-genome-sequencing

Last synced: 10 Apr 2025

https://github.com/ewissel/hamroaster

hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance

amr antibiotic bioinformatics metagenomics microbiology

Last synced: 21 Nov 2024

https://github.com/majsylw/microbial-counting-review

A list of useful resources in the microbial colony classification and detection, such as datasets, papers, links to projects

agar-plate cfu classification datasets density-estimation microbial-colonies microbial-counting microbial-detection microbiology object-detection synthetic-dataset-generation

Last synced: 26 Mar 2025

https://github.com/biosustain/pseudobatch

The Pseudobatch transformation is a method to easy analysis of measurement from a fed-batch fermentation process. After transformation, the data can be analysed as if it was obtained from a batch fermentation process. The Pseudobatch transformation is especially useful for fed-batch processes where samples where drawn from the bioreactor.

fed-batch fermentation fermentation-process microbiology

Last synced: 12 Apr 2025

https://github.com/moshi4/pybarrnap

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

bioinformatics genome-annotation genomics microbial-genomics microbiology python rna

Last synced: 21 Apr 2025

https://github.com/minsithu/burmese-microbiology-1k

Microbiology 1K QA pairs in Burmese Language

artificial-intelligence burmese-gpt dataset microbiology myanmar-language myanmargpt-movement nlp

Last synced: 26 Feb 2025

https://github.com/cameronmartino/bacdivepy

bacdive cultivation microbiology

Last synced: 13 May 2025

https://github.com/snitkin-lab-umich/prewas

R package to perform data pre-processing for more informative bacterial GWAS

bacterial-genomes gwas gwas-tools microbiology r r-package

Last synced: 13 Apr 2025

https://github.com/j-w-yun/plasmid-planner

Automatically plan the most optimal expression vector using restriction enzymes.

cloning dna-sequences microbiology molecular-biology plasmid plasmid-sequences restriction-enzyme

Last synced: 14 May 2025

https://github.com/dmnfarrell/mtbdiff

Characterization of Mycobacterium tuberculosis complex species using mummer and nucdiff

bioinformatics genomics microbiology mycobacterium-tuberculosis

Last synced: 15 Apr 2025

https://github.com/astrabert/distilgpt2-finetuned-microbiology

Small model for language modeling based on distilgpt2 and on microbiology-related text data

academic-project ai automation distilgpt2 finetuned-model generative-ai huggingface huggingface-transformers integrations microbiology text-generation

Last synced: 05 Mar 2025

https://github.com/erictleung/microbiome-analysis-resources

:microscope: Resources and notes on studying the human microbiome

bioinformatics data-analysis gut-microbiome microbiology microbiome notes resources

Last synced: 03 Apr 2025

https://github.com/msberends/a_new_instrument_for_microbial_epidemiology

This is my full PhD thesis in R Markdown (using the bookdown package), containing a PDF and EPUB file, and a website in the ‘docs’ folder with the integral content of the book. The shortened URL is git.io/PhDthesisAMR.

epidemiology microbiology phd-thesis r

Last synced: 28 Mar 2025