bioBakery

bioBakery's repositories

MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

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biobakery

bioBakery tools for meta'omic profiling

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humann

HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

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phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

Language:PythonMIT118 6 113

Maaslin2

MaAsLin2: Microbiome Multivariate Association with Linear Models

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kneaddata

Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

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biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

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graphlan

High-quality circular representations of taxonomic and phylogenetic trees

Language:PythonMIT84 6 9

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.

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metawibele

MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

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halla

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SparseDOSSA2

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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).

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MTX_model

R package for differential expression analysis in metatranscriptomics

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banocc

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anpan

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MMUPHin

MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

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ccrepe

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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