biobakery
There are 0 repository under biobakery topic.
biobakery / MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
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HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
Language:Python 166Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
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Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
Language:Python 106bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
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Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
Language:R 34ShortBRED 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.
Language:Python 28MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome
Language:Python 20AnADAMA2 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).
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Biobakery formulae for the Homebrew package manager
Language:Ruby 10MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies
Language:R 7himelmallick / BenchmarkMicrobiome
Large-scale Benchmarking of Microbial Multivariable Association Methods
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MaAsLin is a multivariate statistical framework that finds associations between clinical metadata and potentially high-dimensional experimental data.
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The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets.
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FUGAsseM: Function predictor of Uncharacterized Gene products by Assessing high-dimensional community data in Microbiomes
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Omnibus and Maaslin2 Rscripts and hmp2-data
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Hierarchical All-against-All association testing is designed as a command-line tool to find associations in high-dimensional, heterogeneous datasets.
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Prioritization and Prediction of functional Annotations for Novel and Important genes via automated data Network Integration
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AroArz / singularity_playground
This repo maintains the definition files used for building singularity images remotely. Each branch maintains a different environment.
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SflE (pronounced "souffle") is a Scientific workFLow Environment built around the SCons build system
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