Topic: "bacteria"
Ecogenomics/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Language: Python - Size: 28.8 MB - Last synced at: about 21 hours ago - Pushed at: about 1 month ago - Stars: 524 - Forks: 85
tseemann/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Language: Perl - Size: 124 MB - Last synced at: 4 days ago - Pushed at: 11 months ago - Stars: 518 - Forks: 117
oschwengers/bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Language: Python - Size: 99.3 MB - Last synced at: 7 days ago - Pushed at: 3 months ago - Stars: 511 - Forks: 62
labgem/PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
Language: Python - Size: 133 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 268 - Forks: 31
AdmiralenOla/Scoary
Pan-genome wide association studies
Language: Python - Size: 2.51 MB - Last synced at: 14 days ago - Pushed at: about 1 year ago - Stars: 196 - Forks: 34
B-UMMI/chewBBACA
BSR-Based Allele Calling Algorithm
Language: HTML - Size: 75.9 MB - Last synced at: 24 days ago - Pushed at: about 2 months ago - Stars: 142 - Forks: 28
tseemann/nullarbor
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
Language: Perl - Size: 11.3 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 139 - Forks: 38
mgalardini/pyseer
SEER, reimplemented in python 🐍🔮
Language: Python - Size: 73.4 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 121 - Forks: 27
oschwengers/platon
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
Language: Python - Size: 37.4 MB - Last synced at: 12 days ago - Pushed at: 4 months ago - Stars: 116 - Forks: 15
Pioreactor/pioreactor
Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.
Language: Python - Size: 11.1 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 114 - Forks: 10
eead-csic-compbio/get_homologues
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
Language: Perl - Size: 79.8 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 112 - Forks: 26
neherlab/pangraph
A bioinformatic toolkit to align genome assemblies into pangenome graphs
Language: C - Size: 75.7 MB - Last synced at: 12 days ago - Pushed at: about 2 months ago - Stars: 106 - Forks: 7
bacpop/PopPUNK
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
Language: Python - Size: 116 MB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 97 - Forks: 20
oschwengers/asap
A scalable bacterial genome assembly, annotation and analysis pipeline
Language: Groovy - Size: 13.6 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 73 - Forks: 19
kjolley/BIGSdb
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
Language: Perl - Size: 385 MB - Last synced at: about 22 hours ago - Pushed at: 1 day ago - Stars: 69 - Forks: 21
cmkobel/CompareM2
🦠📇 Microbial genomes-to-report pipeline
Language: Python - Size: 95.6 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 56 - Forks: 3
nf-core/bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Language: Nextflow - Size: 73.1 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 55 - Forks: 51
voorloopnul/awesome-phages
A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.
Size: 16.6 KB - Last synced at: 28 days ago - Pushed at: almost 3 years ago - Stars: 48 - Forks: 6
johnlees/seer
sequence element (kmer) enrichment analysis
Language: C++ - Size: 1.32 MB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 43 - Forks: 10
CCB-SB/plsdb
PLSDB pipeline to collect bacterial plasmids from NCBI
Language: Python - Size: 13.3 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 35 - Forks: 4
prophyle/prophyle
Accurate, resource-frugal and deterministic DNA sequence classifier.
Language: Python - Size: 30.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 34 - Forks: 5
Zebbeni/protozoa
A simulation of protozoan behavior and evolution
Language: Go - Size: 4.34 MB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 33 - Forks: 6
EngqvistLab/Tome
A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
Language: Python - Size: 50.8 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 32 - Forks: 13
tseemann/phastaf
Identify phage regions in bacterial genomes for masking purposes
Language: Perl - Size: 18.4 MB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 30 - Forks: 4
karel-brinda/Phylign
Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
Language: Python - Size: 7.09 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 27 - Forks: 7
ncrna/PathogenTrack
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.
Language: Python - Size: 59.5 MB - Last synced at: 9 days ago - Pushed at: over 1 year ago - Stars: 27 - Forks: 8
ICBI/viGEN
viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
Language: Shell - Size: 30.3 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 26 - Forks: 15
tseemann/sixess
🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files
Language: Shell - Size: 36.9 MB - Last synced at: about 2 months ago - Pushed at: about 7 years ago - Stars: 24 - Forks: 2
quadram-institute-bioscience/socru
Order and orientation of complete bacterial genomes
Language: Python - Size: 226 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 6
karel-brinda/MiniPhy
Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
Language: Python - Size: 5.85 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 22 - Forks: 1
GunzIvan28/rMAP
Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS
Language: Shell - Size: 6.27 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 22 - Forks: 17
KThorellGroup/BACTpipe
BACTpipe: An assembly and annotation pipeline for bacterial genomics
Language: Groovy - Size: 3.9 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 20 - Forks: 7
oschwengers/tadrep
Targeted Detection and Reconstruction of Plasmids
Language: Python - Size: 2.63 MB - Last synced at: 20 days ago - Pushed at: about 1 year ago - Stars: 20 - Forks: 1
xthua/bacant
This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.
Language: F* - Size: 49.8 MB - Last synced at: 23 days ago - Pushed at: about 2 years ago - Stars: 20 - Forks: 7
mbhall88/NanoVarBench
Evaluating Nanopore-based bacterial variant calling
Language: Python - Size: 37.4 MB - Last synced at: 3 days ago - Pushed at: 29 days ago - Stars: 19 - Forks: 1
phac-nml/mikrokondo
A simple pipeline for bacterial assembly and quality control
Language: Nextflow - Size: 14.4 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 17 - Forks: 3
Danderson123/Amira
A tool to detect acquired AMR genes directly from long read sequencing data.
Language: Python - Size: 15.3 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 14 - Forks: 2
DEMENT-Model/DEMENTpy
A spatially explicit trait- and individual-based microbial systems modelling framework
Language: Python - Size: 29.3 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 14 - Forks: 7
lmc297/bactaxR
Bacterial taxonomy construction and evaluation in R
Language: R - Size: 601 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 3
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.
Language: R - Size: 3.22 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 11 - Forks: 12
microbialman/DDotCounter
Simple counting of bacterial colonies from pictures of plates.
Language: Processing - Size: 27.3 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 11 - Forks: 1
vimarconi/biotracker
Particle detection and tracking - A microswimmer tracker with automatic quantification of change of directions. More info and services: [email protected]
Language: Python - Size: 232 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 10 - Forks: 0
pg-space/panspace
Embedding-based indexing for compact storage, rapid querying, and curation of bacterial pan-genomes
Language: Jupyter Notebook - Size: 22.8 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 10 - Forks: 0
amarinderthind/decontaminer
DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS data analysis, while providing a complete, reliable, and automatic pipeline. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2684-x
Language: Perl - Size: 1.45 MB - Last synced at: about 6 hours ago - Pushed at: about 11 hours ago - Stars: 9 - Forks: 0
m-jahn/genome-scale-models
Genome scale metabolic models in SBML format
Language: HTML - Size: 15.7 MB - Last synced at: 5 days ago - Pushed at: over 3 years ago - Stars: 9 - Forks: 6
fanglab/BEAST
Bacterial Epigenomics Analysis SuiTe
Language: R - Size: 360 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 9 - Forks: 2
adamd3/BactSeq
A nextflow pipeline for performing bacterial RNA-Seq data analysis.
Language: Nextflow - Size: 2.32 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 8 - Forks: 1
ohnosequences/db.rna16s
A comprehensive, compact, and automatically curated 16S database
Language: Scala - Size: 1.38 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 8 - Forks: 0
schwanbeck/YSMR
Bacterial video tracking & analysis
Language: Python - Size: 349 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 7 - Forks: 0
jhayer/baargin
Bacterial Assembly and Antimicrobial Resistance Genes In NextFlow
Language: Nextflow - Size: 15.4 MB - Last synced at: 4 days ago - Pushed at: 8 months ago - Stars: 7 - Forks: 0
deprekate/prfect
Software to predict the occurence of programmed ribosomal frameshifting in bacterial, phage, and viral genomes
Language: Python - Size: 878 MB - Last synced at: about 1 month ago - Pushed at: 8 months ago - Stars: 7 - Forks: 1
JakobStenseke/Artificial-Chemotaxis-in-Dynamic-Environments
Artificial agents developing chemotaxis using probabilistic spiking perceptrons
Language: C# - Size: 32.4 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 7 - Forks: 0
Unlimited-Research-Cooperative/Bacteria-Neural-Network
Neural Net Bacteria - Creating bacterial colonies that will learn to play Pong, Go, DOOM, and encode/decode signals
Size: 10.2 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 6 - Forks: 0
avantonder/bacQC
bacQC is a bioinformatics analysis pipeline for assessing the quality of bacterial isolate sequence data
Language: Nextflow - Size: 17.9 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 5 - Forks: 1
avantonder/assembleBAC-ONT
avantonder/assembleBAC-ONT is a bioinformatics pipeline that de novo assembles and annotates Oxford Nanopore (ONT) long-read sequence data.
Language: Nextflow - Size: 3.16 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 5 - Forks: 0
tomdstanton/bart
bacterial read typer :dna: :skateboard: :microbe:
Language: Python - Size: 60.3 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 5 - Forks: 2
biodatlab/bacteria-detection
Deep Learning-Based Object Detection and Bacteria Morphological Feature Extraction for Antimicrobial Resistance Applications
Language: Python - Size: 216 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 2
voorloopnul/decouphage
The art of decorating a phage genome by gluing feature cutouts into it.
Language: Python - Size: 5.86 MB - Last synced at: 23 days ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 2
8nkit/Leaf-Blight-Detection
To detect bacterial trio in leaf using tensorflowlite implemented in Android
Language: Kotlin - Size: 12.5 MB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 3
Zabuzard/Antigen
Strategy game with cells, bacteria and viruses as units.
Language: C# - Size: 218 MB - Last synced at: 2 months ago - Pushed at: over 9 years ago - Stars: 5 - Forks: 1
FLI_Bioinfo/WGSBAC
Modules for genotyping and characterisation of bacterial isolates utilizing whole-genome-sequencing data
Last synced at: about 2 years ago - Stars: 5 - Forks: 0
alipirani88/snpkit
Modular workflow for Microbial Variant Calling and SNP diagnostics.
Language: Python - Size: 60.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 4
apredeus/multi-bacpipe
A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments
Language: Perl - Size: 2.15 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 2
iferres/simurg
Simulate pangenomes according to the IMG + Neutral models
Language: R - Size: 382 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 4 - Forks: 1
Bobay-Ochman/ConSpeciFix
A process to better define speciation
Language: Python - Size: 14.4 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 4 - Forks: 1
karel-brinda/phylogenetic-compression-supplement
Supplementary repository for "Efficient and robust search of microbial genomes via Phylogenetic Compression"
Language: Python - Size: 34 MB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 3 - Forks: 0
iman2693/CTCB
This is the repository for the CTCB project
Language: Jupyter Notebook - Size: 192 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0
Unlimited-Research-Cooperative/Human-Brain-Organoid-Bacterial-Neural-Link
Bacterial colonies attaching themselves to human brain organoids, as a neural link to a silicon computer
Size: 5.86 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0
JakubBartoszewicz/DeePaC
Predicting pathogenic potentials of short DNA reads with reverse-complement deep neural networks.
Language: Jupyter Notebook - Size: 163 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 2
bioatmosphere/microbiome-drought-legacy
A theorectical investigation into mechanisms of drought legacy formation and influencing factors in soil microbiomes using DEMENTpy.
Language: Jupyter Notebook - Size: 329 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0
mastrof/Bactos.jl
Agent-based modeling framework for bacterial behavior, based on Agents.jl
Language: Julia - Size: 2.53 MB - Last synced at: 8 months ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 0
nlabrad/CIMS-Cyanobacterial-ITS-motif-slicer
A tool to identify and extract the commonly used ITS folding motifs from a 16s-23s rRNA sequence.
Language: Python - Size: 6.06 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1
creativequotient/mathsysbio
DMS1401ZB Mathematical Systems Biology
Language: Jupyter Notebook - Size: 831 KB - Last synced at: about 6 hours ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 5
amarinderthind/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.
Language: R - Size: 1.17 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 2 - Forks: 2
onco-p53/manuscripts
Code and data for my scientific publications
Language: R - Size: 919 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0
Godrigos/mediadb
A small android application project listing commonly used microbiology culture media.
Language: Dart - Size: 2.04 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 0
EngqvistLab/orgtools
A library to get information on organisms and UniProt identifiers. This includes growth temperature, growth ph, pfam domains, taxonomic lineage.
Language: Python - Size: 275 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 2 - Forks: 0
tgolubch/castanet
Data processing scripts for analysis of targeted metagenomics sequencing data. Intended for use with multiplexed Illumina short-read data generated after enrichment.
Language: Python - Size: 27.3 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 2 - Forks: 1
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.
Language: Jupyter Notebook - Size: 7.77 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0
moorembioinfo/FlexCore
Extract flexible bacterial core genome alignments and compute SNP distances. Additionally, perform rarefaction-sampling analysis of alignments
Language: Python - Size: 49.8 KB - Last synced at: 7 days ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0
baynec2/nanopore_pipelines
Nanopore sequencing experimental protocols and computational pipelines
Language: Shell - Size: 333 KB - Last synced at: 21 days ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0
lisavader/plasmidEC
An ensemble of plasmid classification tools
Language: Shell - Size: 11.7 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 2
xlxs4/bacteria-phage-montecarlo
A toy MC model studying bacteria-phage coevolution dynamics. Code is meant to be readable instead of performant, or, well, good. Good for beginners in ABM
Language: Python - Size: 3.91 KB - Last synced at: 3 days ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0
sandain/ecosim
Ecotype Simulation: Models the sequence diversity within a bacterial clade.
Language: Java - Size: 18.3 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1
rtsearcy/NowCast
The NowCast System - Predictive modeling of water quality at California beaches
Language: Python - Size: 799 KB - Last synced at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 2 - Forks: 0
emanuelhuber/gwModBac
Groundwater flow and microbes transport modelling with R and Modflow / Modpath
Language: R - Size: 3.4 MB - Last synced at: 3 months ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 1
nvladimus/rapidcell
Multiscale modeling of E.coli chemotaxis
Language: Jupyter Notebook - Size: 1.16 MB - Last synced at: 3 months ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 1
romagnolid/combact 📦
Pipeline to highlight genomic mutations in bacterial genomes
Language: Python - Size: 105 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0
TheOpenBacteriaProject/Biological-Documentation
This repository contains all documentation about theoric biological issues such as culture methods and techniques, justification, ecology and current functions of chosen microorganisms
Size: 5.28 MB - Last synced at: over 2 years ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 0
SchlossLab/Hannigan_ConjunctisViribus_ploscompbio_2018
Using graph database techniques to understand the infectious relationships between bacteria and phages.
Language: PostScript - Size: 449 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 4
snewhouse/exotic-dna-ngs
WIP & POC: Count Viral and other non-human genome signatures in Human NGS data
Language: Shell - Size: 114 KB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 2 - Forks: 0
RolandR/bacteria
What started out as a terrain generator ended up being something akin to bacteria growing in a petri dish.
Language: JavaScript - Size: 3.91 KB - Last synced at: about 2 years ago - Pushed at: almost 9 years ago - Stars: 2 - Forks: 2
rki_bioinformatics/DeePaC
Predicting pathogenic potentials of short DNA reads with reverse-complement deep neural networks.
Last synced at: about 2 months ago - Stars: 2 - Forks: 5
avantonder/assembleBAC
avantonder/assembleBAC is a bioinformatics best-practise analysis pipeline for assembling and annotating bacterial genomes.
Language: Nextflow - Size: 4.06 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0
avantonder/bacQC-ONT
bacQC-ONT is a bioinformatics pipeline for the assessment of Oxford Nanopore sequence data
Language: Nextflow - Size: 2.74 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0
bacpop/bacpop-website
Code for group website
Language: HTML - Size: 47.8 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 1 - Forks: 7
climatechangemicrobiology/ProGRN
Prokaryote Gene Regulatory Network (ProGRN) Inference Pipeline
Language: HTML - Size: 238 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0
EngineerDanny/CS685-Microbe-Network-Research-Code
This repo contains my cross-validation ML analysis for training and testing co-occurrence network inference algorithms
Language: Jupyter Notebook - Size: 12.9 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0
ShawnKyzer/data-pipeline-microbiom-duckdb
A high-performance data pipeline built with Python and DuckDB for processing and analyzing Human Microbiome Project (HMP) bacterial genome data. Features include automated GenBank file processing, Prefect workflow orchestration, an interactive Streamlit dashboard for data exploration, and comprehensive test coverage. Perfect for bio researchers.
Language: Python - Size: 1.75 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0
adamd3/StrainQuant
A Nextflow pipeline for performing bacterial RNA-Seq analysis without a reference genome.
Language: Nextflow - Size: 30.7 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0