Projects in Awesome Lists tagged with biobakery
A curated list of projects in awesome lists tagged with biobakery .
https://github.com/biobakery/biobakery
bioBakery tools for meta'omic profiling
Last synced: 16 May 2025
https://github.com/biobakery/metaphlan
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
biobakery metagenomics public python tools
Last synced: 12 Apr 2025
https://github.com/biobakery/humann
HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
Last synced: 06 Apr 2025
https://github.com/biobakery/phylophlan
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
biobakery phylogenetic-trees python tools
Last synced: 16 May 2025
https://github.com/biobakery/maaslin2
MaAsLin2: Microbiome Multivariate Association with Linear Models
biobakery bioconductor differential-abundance-analysis false-discovery-rate metagenomics microbiome multiple-covariates public repeated-measures tools
Last synced: 04 Apr 2025
https://github.com/biobakery/kneaddata
Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
biobakery bowtie2 kneaddata public quality-control tools
Last synced: 05 Apr 2025
https://github.com/biobakery/biobakery_workflows
bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
analysis-workflows biobakery private
Last synced: 05 Apr 2025
https://github.com/biobakery/graphlan
High-quality circular representations of taxonomic and phylogenetic trees
biobakery circular-visualization phylogenetic-trees python taxonomic-trees tools
Last synced: 10 Apr 2025
https://github.com/biobakery/melonnpan
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
biobakery bioconductor machine-learning metabolite-compounds metabolite-prediction metabolomics metagenomics microbial-communities microbiome multi-omics public tools
Last synced: 14 Apr 2025
https://github.com/biobakery/shortbred
ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.
Last synced: 14 Apr 2025
https://github.com/biobakery/sparsedossa2
biobakery bioconductor public tools
Last synced: 15 Mar 2025
https://github.com/biobakery/homebrew-biobakery
Biobakery formulae for the Homebrew package manager
Last synced: 14 Apr 2025
https://github.com/biobakery/anadama2
AnADAMA2 is the next generation of AnADAMA (Another Automated Data Analysis Management Application). AnADAMA is a tool to capture your workflow and execute it efficiently on your local machine or in a grid compute environment (ie. sun grid engine or slurm).
Last synced: 14 Apr 2025
https://github.com/biobakery/mmuphin
MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies
biobakery bioconductor public tools
Last synced: 14 Apr 2025
https://github.com/biobakery/maaslin
MaAsLin is a multivariate statistical framework that finds associations between clinical metadata and potentially high-dimensional experimental data.
Last synced: 14 Apr 2025
https://github.com/biobakery/sparsedossa
biobakery bioconductor public tools
Last synced: 14 Apr 2025
https://github.com/biobakery/ccrepe
The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets.
biobakery bioconductor public tools
Last synced: 15 Mar 2025
https://github.com/biobakery/fugassem
FUGAsseM: Function predictor of Uncharacterized Gene products by Assessing high-dimensional community data in Microbiomes
Last synced: 14 Apr 2025
https://github.com/biobakery/omnibus-and-maaslin2-rscripts-and-hmp2-data
Omnibus and Maaslin2 Rscripts and hmp2-data
archive biobakery public tools
Last synced: 14 Apr 2025
https://github.com/biobakery/conda-biobakery
A collection of conda build recipes
Last synced: 14 Apr 2025
https://github.com/biobakery/firecloud-graphql
GraphQL server and utilities scripts for the BIOM-Mass portal
Last synced: 15 Mar 2025
https://github.com/biobakery/ppanini
Prioritization and Prediction of functional Annotations for Novel and Important genes via automated data Network Integration
Last synced: 15 Mar 2025
https://github.com/biobakery/halla_legacy
Hierarchical All-against-All association testing is designed as a command-line tool to find associations in high-dimensional, heterogeneous datasets.
Last synced: 15 Mar 2025
https://github.com/biobakery/ffpeexampledata
archived biobakery public tools
Last synced: 15 Mar 2025
https://github.com/biobakery/sfle
SflE (pronounced "souffle") is a Scientific workFLow Environment built around the SCons build system
Last synced: 15 Mar 2025
https://github.com/biobakery/physalia-workshop
Stab at a github.io page for the Physalia Workshop
Last synced: 15 Mar 2025