biobakery/shortbred

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28
Rank 877,421 (Top 18 %)
Language
Python
Created over 4 years ago
Updated 6 months ago

biobakery/shortbred

biobakery

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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.

MetaPhlAn

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

biobakery

bioBakery tools for meta'omic profiling

humann

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

phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

Maaslin2

MaAsLin2: Microbiome Multivariate Association with Linear Models

kneaddata

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

biobakery_workflows

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

graphlan

High-quality circular representations of taxonomic and phylogenetic trees

melonnpan

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

MetaPhlAn2

metawibele

MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

SparseDOSSA2

halla

homebrew-biobakery

Biobakery formulae for the Homebrew package manager

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).

MTX_model

R package for differential expression analysis in metatranscriptomics

banocc

MMUPHin

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

maaslin

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

anpan

sparseDOSSA

ccrepe

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

ibd_paper

hmp2_analysis

meddiet2020

micropita

cgfp

uniref_annotator

waafle

http://huttenhower.sph.harvard.edu/waafle

Macarron

omnibus-and-maaslin2-rscripts-and-hmp2-data

Omnibus and Maaslin2 Rscripts and hmp2-data

humann_legacy

maaslin2_benchmark

Large-scale Benchmarking of Microbial Multivariable Association Methods

breadcrumbs

galaxy_lefse

crc-subtyping-paper

parathaa

Preserving and Assimilating Region-specific Ambiguities in Taxonomic Hierarchical Assignments for Amplicons (Parathaa)

fugassem

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

halla_legacy

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

MTX_synthetic

Synthetic data generation for the mtx2021 project

jdrf2

pouchitis

synmetap

galaxy-upgrade

ibd_meta_analysis

sparsedossa_paper

conda-biobakery

A collection of conda build recipes

qiimetomaaslin

ppanini

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

Physical-activity-gut-microbiome-body-weight

maaslin3

MaAsLin3: Microbiome Multivariate Association with Linear Models