biobakery
There are 54 repositories under biobakery topic.
biobakery/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
biobakery/biobakery
bioBakery tools for meta'omic profiling
biobakery/humann
HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
biobakery/phylophlan
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
biobakery/Maaslin2
MaAsLin2: Microbiome Multivariate Association with Linear Models
biobakery/kneaddata
Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
biobakery/biobakery_workflows
bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
biobakery/graphlan
High-quality circular representations of taxonomic and phylogenetic trees
biobakery/melonnpan
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
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.
biobakery/metawibele
MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome
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).
biobakery/homebrew-biobakery
Biobakery formulae for the Homebrew package manager
biobakery/MMUPHin
MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies
himelmallick/BenchmarkMicrobiome
Large-scale Benchmarking of Microbial Multivariable Association Methods
biobakery/maaslin
MaAsLin is a multivariate statistical framework that finds associations between clinical metadata and potentially high-dimensional experimental data.
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/fugassem
FUGAsseM: Function predictor of Uncharacterized Gene products by Assessing high-dimensional community data in Microbiomes
biobakery/omnibus-and-maaslin2-rscripts-and-hmp2-data
Omnibus and Maaslin2 Rscripts and hmp2-data
biobakery/conda-biobakery
A collection of conda build recipes
biobakery/halla_legacy
Hierarchical All-against-All association testing is designed as a command-line tool to find associations in high-dimensional, heterogeneous datasets.
biobakery/ppanini
Prioritization and Prediction of functional Annotations for Novel and Important genes via automated data Network Integration
AroArz/singularity_playground
This repo maintains the definition files used for building singularity images remotely. Each branch maintains a different environment.
biobakery/sfle
SflE (pronounced "souffle") is a Scientific workFLow Environment built around the SCons build system