microbiology

There are 25 repositories under microbiology topic.

microbiome / microbiome
microbiome R package
microbiome microbiology microbiome-analysis r phyloseq human-microbiome population-study hitchip hitchip-atlas
Language:R 285
pyGenomeViz
moshi4 / pyGenomeViz
A genome visualization python package for comparative genomics
bioinformatics comparative-genomics matplotlib microbial-genomics genomics genomics-visualization genbank python visualization synteny microbiology gff gff3
Language:Python 270
MrOlm / drep
Rapid comparison and dereplication of genomes
assembly bioinformatics metagenomics microbial-genomes microbiology
Language:Python 247
PPanGGOLiN
labgem / PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
comparative-genomics bioinformatics microbial-genomics microbiology bacteria pangenome
Language:Python 237
platon
oschwengers / platon
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
microbiology bioinformatics plasmids ngs wgs contigs bacteria assembly
Language:Python 106
referenceseeker
oschwengers / referenceseeker
Rapid determination of appropriate reference genomes.
bioinformatics reference-genomes mash refseq wgs microbiology ani
Language:Python 88
AMR
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.
r microbiology epidemiology antimicrobial-data amr software
Language:R 83
qgeissmann / OpenCFU
An easy-to-use C++ application to count bacterial colonies (i.e. CFU).
count-bacterial-colonies cplusplus microbiology opencv
Language:C++ 80
EngqvistLab / Tome
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
microbiology temperature-data enzymes machine-learning bioinformatics bacteria archaea eukaryotes
Language:Python 52
vinuesa / get_phylomarkers
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
phylogenomics population-genetics phylogenomics-pipeline species-trees markers genomics pipeline phylogenetics phylogenetic-trees codon-alignment maximum-likelihood orthologues species-delimitation microbiology core-genome perl r bash clock-hypothesis recombination
Language:Perl 51
rdpstaff / RDPTools
Collection of commonly used RDP Tools for easy building
16s bayesian-classifiers bioinformatics microbiology microbiome sequence-alignment
Language:Makefile 49
aleimba / bac-genomics-scripts
Collection of scripts for bacterial genomics
perl bioinformatics genomics science microbial-genomics microbiology ngs sequencing annotation mlst blast unix bioperl scripts-collection opensource computational-biology
Language:Perl 42
BU-ISCIII / plasmidID
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
plasmid ngs ngs-analysis microbiology whole-genome-sequencing
Language:Shell 37
dmnfarrell / teaching
scripts and notes for learning
bioinformatics python pyviz bokeh jupyter microbiology
Language:Jupyter Notebook 36
Geo-omics / scripts
Metagenomic pipeline and other general scripts used in the lab.
perl umich python geomicrobiology microbiology ngs-analysis
Language:Perl 34
gan
telatin / gan
📜 the Great Automatic Nomenclator — The Next Million Names for Archaea and Bacteria
bacterial-genomes bacterial-names database greek latin microbiology nomenclature python3 taxonomy
Language:Python 32
IDBacApp
chasemc / IDBacApp
A MALDI Mass Spectrometry Bioinformatics Platform
mass-spectrometry microbiology r shiny
Language:R 28
JTFouquier / ghost-tree
creating hybrid-gene phylogenetic trees for diversity analyses
python python3 phylogenetics phylogenetic-trees diversity fungi fungal microbiome microbiology microbial-ecology bioinformatics
Language:Python 28
jlumpe / gambit
A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
bioinformatics genomics microbiology public-health whole-genome-sequencing
Language:Python 26
dr-joe-wirth / phantasm
PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
bioinformatics phylogenomics taxonomy microbiology
Language:Python 21
ewissel / hAMRoaster
hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance
antibiotic amr microbiology metagenomics bioinformatics
Language:Python 21
vallenderlab / MicrobiomeR
A comprehensive and customizable R package for microbiome analysis.
microbiome microbial-genomics microbiome-analysis phyloseq metacoder r rstats visualization color-palette bioinformatics permanova alpha-diversity beta-diversity pcoa comprehensive metagenomics microbiology
Language:R 20
genotoul-bioinfo / Binette
A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.
bioinformatics-tool metagenomics-binning metagenomics microbiology
Language:Python 16
Knowledge-Graph-Hub / kg-microbe
knowledge-graph anatomical-knowledge chebi chemicals environments envo go media metabolism microbiology phenotypes traits cell-shapes ncbitaxonomy data-modeling named-entity-recognition nlp oaklib robot
Language:Jupyter Notebook 15
frubino / mgkit
MGKit: Metagenomics Framework
bioinformatics metagenomic-pipeline metagenomics microbiology
Language:Python 14
microbialman / DDotCounter
Simple counting of bacterial colonies from pictures of plates.
bacteria bacterial-counts counting image-processing image-segmentation microbiology processing segmentation
Language:Processing 13
moshi4 / pybarrnap
Python implementation of barrnap (Bacterial ribosomal RNA predictor)
bioinformatics genome-annotation genomics microbial-genomics microbiology python rna
Language:Python 13
mshamash / OnePetri
Accelerate common Petri dish assays with AI.
petri-dish phage plaque computer-vision artificial-intelligence yolov5 ios-app biomedical-research swift microbiology machine-learning object-detection
Language:Swift 13
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
12
TIBHannover / BacDiveR
Inofficial R client for the DSMZ's Bacterial Diversity Metadatabase (former contact: @katrinleinweber). https://api.bacdive.dsmz.de/client_examples seems to be the official alternatives.
r microorganism bacterial-database bacteriology webservice-client microbiology biobank r-package rstats bacterial-samples rlang rlanguage bacterial diversity bacteria api-client bacdive
Language:R 10
NadjaKry / WGS_pipeline
Bacterial whole genome sequencing (WGS) analysis
genomics whole-genome-sequencing microbiology bioinformatics
Language:Shell 8
spiro
jonasoh / spiro
SPIRO is a Smart Plate Imaging Robot
science biology microbiology raspberry-pi arabidopsis biological-imaging plant-science open-hardware
Language:Python 7
m-jahn / genome-scale-models
Genome scale metabolic models in SBML format
genome-scale-models computational-biology python3 sbml-models microbiology bacteria
Language:HTML 7
schwanbeck / YSMR
Bacterial video tracking & analysis
opencv-python bacteria-motion-depending bacteria tracking display-video-analysis microbiology python3 matplotlib seaborn pandas numpy scipy xlsxwriter video
Language:Python 7
Burmese-Microbiology-1K
MinSiThu / Burmese-Microbiology-1K
Microbiology 1K QA pairs in Burmese Language
artificial-intelligence burmese-gpt dataset microbiology myanmar-language myanmargpt-movement nlp
6
mshamash / OnePetri-models
Repository containing trained YOLOv5 object detection models used within OnePetri for Petri dish and plaque detection.
yolov5 computer-vision object-detection phage plaque petri-dish microbiology biomedical-research artificial-intelligence machine-learning
6