Search Results - RepositoryStats

vsearch torognes

124

675

other

43

Versatile open-source tool for microbiome analysis

fasta fastq search chimera amplicon clustering microbiome metagenomics metabarcoding bioinformatics sequence-alignment

Created 2014-05-16

3,288 commits to master branch, last one 15 days ago

dada2 benjjneb

144

474

lgpl-3.0

39

Accurate sample inference from amplicon data with single nucleotide resolution

amplicon taxonomy microbiome bioconductor metagenomics metabarcoding bioinformatics

Created 2014-12-17

797 commits to master branch, last one a day ago

microbiome microbiome

55

289

other

33

microbiome R package

r hitchip phyloseq microbiome microbiology hitchip-atlas human-microbiome population-study microbiome-analysis

Created 2012-08-07

2,228 commits to master branch, last one about a year ago

qiime biocore

265

286

gpl-2.0

57

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

analysis microbiome

This repository has been archived (exclude archived)

Created 2012-10-14

7,718 commits to master branch, last one 6 years ago

DRAM WrightonLabCSU

52

259

gpl-3.0

6

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

genomics annotation microbiome metagenomics bioinformatics viral-genomics viral-metagenomics metagenome-assembled-genomes

Created 2019-02-11

867 commits to master branch, last one 29 days ago

metaGEM franciscozorrilla

43

206

mit

5

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

mags snakemake metabolism microbiome metagenomics bioinformatics gut-microbiome systems-biology metabolic-models microbial-ecology metabolic-modeling computational-biology flux-balance-analysis genome-scale-metabolic-model metagenome-assembled-genomes

Created 2018-06-14

669 commits to master branch, last one 4 months ago

ampliseq nf-core

119

188

mit

153

Amplicon sequencing analysis workflow using DADA2 and QIIME2

16s 18s its edna rrna pacbio qiime2 nf-core illumina nextflow pipeline workflow iontorrent microbiome metagenomics metabarcoding amplicon-sequencing taxonomic-profiling taxonomic-classification

Created 2018-09-26

2,541 commits to master branch, last one 18 days ago

MicrobiotaProcess YuLab-SMU

37

183

unknown

8

:microbe: A comprehensive R package for deep mining microbiome

rstats microbiome microbiome-data microbiome-analysis

Created 2019-03-01

1,343 commits to master branch, last one 29 days ago

microbiomeMarker yiluheihei

40

171

gpl-3.0

11

R package for microbiome biomarker discovery

r lefse r-package microbiome metagenomics biomarker-discovery differential-abundance-analysis

Created 2019-10-17

269 commits to devel branch, last one about a year ago

HumanMicrobiome MaximilianKohler

11

156

unknown

13

Human Microbiome wiki

health science microbiome

Created 2019-05-18

57 commits to master branch, last one about a year ago

decontam benjjneb

25

148

unknown

12

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

amplicon microbiome metagenomics contamination metabarcoding bioinformatics

Created 2017-04-04

78 commits to master branch, last one 3 years ago

pandora genular

21

135

other

11

PANDORA :computer:

tsne umap pandora biomarkers clustering microbiome data-mining data-science clinical-data bioinformatics drug-discovery systems-biology transcriptomics data-integration machine-learning data-visualization predictive-analytics genomic-data-analysis unsupervised-machine-learning

Created 2018-07-03

1,546 commits to master branch, last one 19 days ago

taxprofiler nf-core

36

129

mit

156

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

nf-core shotgun illumina nanopore nextflow pathogen pipeline workflow profiling long-reads microbiome metagenomics bioinformatics classification taxonomic-profiling taxonomic-classification

Created 2022-02-18

2,031 commits to master branch, last one 5 days ago

swarm torognes

23

127

agpl-3.0

14

A robust and fast clustering method for amplicon-based studies

fasta sequence clustering microbiome metabarcoding bioinformatics

Created 2012-11-10

2,935 commits to master branch, last one 7 months ago

Maaslin2 biobakery

35

123

other

8

MaAsLin2: Microbiome Multivariate Association with Linear Models

tools public biobakery microbiome bioconductor metagenomics repeated-measures multiple-covariates false-discovery-rate differential-abundance-analysis

Created 2019-05-14

523 commits to master branch, last one 22 days ago

qiita qiita-spots

80

121

bsd-3-clause

21

Qiita - A multi-omics databasing effort

python microbiome microbiome-analysis

Created 2013-09-26

7,804 commits to master branch, last one about a month ago

ggpicrust2 cafferychen777

13

111

mit

2

Make Picrust2 Output Analysis and Visualization Easier

16s-rrna picrust2 tax4fun2 microbiome microbiota metagenomics visualization functional-data metagenomic-analysis

Created 2022-12-17

284 commits to main branch, last one 5 days ago

MicrobiomeBestPracticeReview grimmlab

38

109

mit

4

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

16s-rrna assembly pipeline biomedical microbiome metagenomics best-practices bioinformatics amplicon-sequencing microbiome-analysis microbiome-workflow

Created 2018-11-16

101 commits to master branch, last one 6 months ago

ANCOMBC FrederickHuangLin

29

108

unknown

8

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

ancom secom ancombc ancombc2 microbiome sequencing correlation normalization differential-abundance-analysis

Created 2020-08-10

84 commits to bugfix branch, last one about a month ago

microViz david-barnett

11

107

gpl-3.0

6

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

r rstats microbiome microbiota microbiome-analysis

Created 2020-10-25

878 commits to main branch, last one 15 days ago

micom micom-dev

18

94

apache-2.0

5

Python package to study microbial communities using metabolic modeling.

flux cobra python cobrapy modeling community microbiome microbiota biochemistry hacktoberfest systems-biology metabolic-models

Created 2017-02-14

811 commits to main branch, last one 8 days ago

sccomp MangiolaLaboratory

7

94

gpl-3.0

8

Testing differences in cell type proportions from single-cell data.

cytof bayesian r-package microbiome multilevel composition proportions single-cell random-effects batch-correction unwanted-variation differential-proportion

Created 2021-02-08

1,582 commits to master branch, last one a day ago

ganon pirovc

13

87

mit

4

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierar...

gtdb ncbi k-mer refseq genbank taxonomy microbiome minimizers bloom-filter metagenomics bioinformatics

Created 2018-08-30

690 commits to master branch, last one 9 months ago

OMA microbiome

42

86

unknown

11

Orchestrating Microbiome Analysis

r microbiome bioconductor microbiome-analysis-book

Created 2020-11-02

892 commits to devel branch, last one a day ago

DeepMicrobes MicrobeLab

21

85

apache-2.0

6

DeepMicrobes: taxonomic classification for metagenomics with deep learning

microbiome metagenomics deep-learning bioinformatics next-generation-sequencing

Created 2019-07-03

49 commits to master branch, last one 2 years ago

veba jolespin

9

78

agpl-3.0

4

A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

genomics microbial microbiome metagenomics bioinformatics metatranscriptomics

Created 2022-04-20

460 commits to main branch, last one 2 months ago

gemelli biocore

17

76

bsd-3-clause

7

Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse ...

ctf rclr rpca qiime2 tempted joint-rpca microbiome compositional-data-analysis

Created 2019-02-14

359 commits to master branch, last one 2 months ago

FlashWeave.jl meringlab

8

74

other

7

Inference of microbial interaction networks from large-scale heterogeneous abundance data

julia metadata microbiome co-occurence metagenomics bioinformatics compositional-data ecological-network high-performance-computing probabilistic-graphical-models

Created 2017-03-06

418 commits to master branch, last one 6 months ago

woltka qiyunzhu

25

71

bsd-3-clause

9

Woltka: a versatile meta'omic data classifier

microbiome metagenomics bioinformatics

Created 2020-01-20

542 commits to main branch, last one about a month ago

microbiomeExplorer zoecastillo

21

69

other

9

The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph...

microbiome microbiome-analysis

Created 2020-07-27

37 commits to master branch, last one 2 years ago