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).

Language: Python - Size: 4.27 MB - Last synced: about 20 hours ago - Pushed: 1 day ago - Stars: 9 - Forks: 3

biobakery/MetaPhlAn

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

Language: Python - Size: 6.7 MB - Last synced: 3 days ago - Pushed: 9 days ago - Stars: 270 - Forks: 75

biobakery/firecloud-graphql

GraphQL server and utilities scripts for the BIOM-Mass portal

Language: Python - Size: 280 KB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 1

biobakery/phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

Language: Python - Size: 112 MB - Last synced: 8 days ago - Pushed: about 1 month ago - Stars: 113 - Forks: 32

biobakery/metawibele

MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

Language: Python - Size: 203 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 18 - Forks: 3

biobakery/jdrf2

Language: HTML - Size: 8.75 MB - Last synced: about 2 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 0

biobakery/portal-ui Fork of IGS/portal-ui

BIOM-Mass Data Portal UI (developed from the NCI-GDC portal UI framework)

Language: JavaScript - Size: 12.1 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 1

biobakery/homebrew-biobakery

Biobakery formulae for the Homebrew package manager

Language: Ruby - Size: 171 KB - Last synced: about 2 months ago - Pushed: over 4 years ago - Stars: 10 - Forks: 4

biobakery/fugassem

FUGAsseM: Function predictor of Uncharacterized Gene products by Assessing high-dimensional community data in Microbiomes

Language: Python - Size: 17 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

biobakery/banocc

Language: TeX - Size: 84.5 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 6 - Forks: 0

biobakery/MMUPHin

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

Language: R - Size: 2.68 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 4 - Forks: 4

biobakery/biobakery

bioBakery tools for meta'omic profiling

Language: Shell - Size: 789 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 246 - Forks: 70

biobakery/kneaddata

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

Language: Python - Size: 1000 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 97 - Forks: 28

biobakery/graphlan

High-quality circular representations of taxonomic and phylogenetic trees

Language: Python - Size: 2.68 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 82 - Forks: 28

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.

Language: Python - Size: 4.03 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 22 - Forks: 5

biobakery/Maaslin2

MaAsLin2: Microbiome Multivariate Association with Linear Models

Language: R - Size: 1.15 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 96 - Forks: 34

biobakery/melonnpan

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

Language: R - Size: 3.81 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 33 - Forks: 8

biobakery/humann

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

Language: Python - Size: 1.57 GB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 142 - Forks: 52

biobakery/biobakery_workflows

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

Language: Python - Size: 321 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 92 - Forks: 32

biobakery/SparseDOSSA2

Language: HTML - Size: 22.3 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 10 - Forks: 2

biobakery/halla_legacy

Hierarchical All-against-All association testing is designed as a command-line tool to find associations in high-dimensional, heterogeneous datasets.

Language: Python - Size: 30.9 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

biobakery/ffpe

Language: R - Size: 16.9 MB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

biobakery/maaslin

MaAsLin is a multivariate statistical framework that finds associations between clinical metadata and potentially high-dimensional experimental data.

Language: R - Size: 2.83 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 6 - Forks: 1

biobakery/qiimetomaaslin

Language: Python - Size: 32.2 KB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

biobakery/galaxy_metaphlan2

Language: Python - Size: 16.6 KB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

biobakery/sparseDOSSA

Language: R - Size: 614 KB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 5 - Forks: 2

broadinstitute/hmp2-ibdmdb-results

Language: Python - Size: 14.3 MB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

broadinstitute/hmp2-ibdmdb-cms

Language: HTML - Size: 15.1 MB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

biobakery/ppanini

Prioritization and Prediction of functional Annotations for Novel and Important genes via automated data Network Integration

Language: UnrealScript - Size: 103 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

himelmallick/BenchmarkMicrobiome

Large-scale Benchmarking of Microbial Multivariable Association Methods

Language: R - Size: 129 KB - Last synced: 14 days ago - Pushed: over 3 years ago - Stars: 7 - Forks: 3

biobakery/ccrepe

The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets.

Language: R - Size: 223 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 3 - Forks: 0

biobakery/physalia-workshop

Stab at a github.io page for the Physalia Workshop

Language: CSS - Size: 56.5 MB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

biobakery/humann_legacy

Language: Python - Size: 201 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 2 - Forks: 0

biobakery/cgfp

Language: Python - Size: 5.66 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 3 - Forks: 1

biobakery/omnibus-and-maaslin2-rscripts-and-hmp2-data

Omnibus and Maaslin2 Rscripts and hmp2-data

Language: R - Size: 4.61 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 5

biobakery/conda-biobakery

A collection of conda build recipes

Language: Shell - Size: 73.2 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 1

biobakery/bioconda-recipes Fork of bioconda/bioconda-recipes

Conda recipes for the bioconda channel.

Language: Shell - Size: 299 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

biobakery/galaxy_lefse

Language: Python - Size: 978 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 2

AroArz/singularity_playground

This repo maintains the definition files used for building singularity images remotely. Each branch maintains a different environment.

Size: 25.4 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 1

biobakery/synmetap

Language: Python - Size: 28.6 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

biobakery/jdrf1

Language: JavaScript - Size: 4.95 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 1

biobakery/docent

Language: Python - Size: 6.84 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

biobakery/sfle

SflE (pronounced "souffle") is a Scientific workFLow Environment built around the SCons build system

Language: Python - Size: 1.5 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

biobakery/microbiomebenchmarking

Language: R - Size: 32.2 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 1

biobakery/galaxy_metaphlan

Size: 261 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

biobakery/galaxy_ccrepe

Language: Python - Size: 198 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

biobakery/galaxy_graphlan

Language: Python - Size: 59.6 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

biobakery/ffpeexampledata

Size: 6.57 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

biobakery/uniref_annotator

Language: Python - Size: 12.7 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1

biobakery/papers

Size: 16.9 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

biobakery/multi-omic

Language: R - Size: 2.57 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

biobakery/hmp2_workflows

Language: Python - Size: 431 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

biobakery/mpuri

Language: R - Size: 39.1 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

biobakery/cutlass Fork of ihmpdcc/cutlass

An iHMP domain specific API using osdf-python

Language: Python - Size: 1000 KB - Last synced: 12 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0