37 results found Sort:

torognes
vsearch torognes
122
643
other
44
Versatile open-source tool for microbiome analysis
fasta fastq search chimera amplicon clustering microbiome metagenomics metabarcoding bioinformatics sequence-alignment
Created 2014-05-16
1,919 commits to master branch, last one about a month ago
benjjneb
dada2 benjjneb
141
460
lgpl-3.0
41
Accurate sample inference from amplicon data with single nucleotide resolution
amplicon taxonomy microbiome bioconductor metagenomics metabarcoding bioinformatics
Created 2014-12-17
782 commits to master branch, last one about a month ago
biocore
qiime biocore
269
285
gpl-2.0
58
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This repository has been archived (exclude archived)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
microbiome
microbiome microbiome
53
275
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 11 months ago
WrightonLabCSU
DRAM WrightonLabCSU
50
239
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
865 commits to master branch, last one 5 months ago
franciscozorrilla
metaGEM franciscozorrilla
37
176
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
665 commits to master branch, last one 5 months ago
YuLab-SMU
MicrobiotaProcess YuLab-SMU
35
167
unknown
8
:microbe: A comprehensive R package for deep mining microbiome
rstats microbiome microbiome-data microbiome-analysis
Created 2019-03-01
1,338 commits to master branch, last one about a month ago
yiluheihei
microbiomeMarker yiluheihei
40
166
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 7 months ago
nf-core
ampliseq nf-core
107
162
mit
148
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
2,467 commits to master branch, last one 2 days ago
MaximilianKohler
HumanMicrobiome MaximilianKohler
10
152
unknown
13
Human Microbiome wiki
health science microbiome
Created 2019-05-18
57 commits to master branch, last one 10 months ago
benjjneb
decontam benjjneb
24
140
unknown
11
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 2 years ago
genular
pandora genular
21
133
other
11
PANDORA - Predictive Analytics aNd Data Oriented Research Applications :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
1,361 commits to master branch, last one 2 months ago
torognes
swarm torognes
23
121
agpl-3.0
13
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 2 months ago
qiita-spots
qiita qiita-spots
80
119
bsd-3-clause
21
Qiita - A multi-omics databasing effort
python microbiome microbiome-analysis
Created 2013-09-26
7,750 commits to master branch, last one 4 months ago
biobakery
Maaslin2 biobakery
35
108
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
519 commits to master branch, last one 4 days ago
nf-core
taxprofiler nf-core
32
104
mit
148
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
1,784 commits to master branch, last one 8 days ago
grimmlab
MicrobiomeBestPracticeReview grimmlab
36
103
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 about a month ago
FrederickHuangLin
ANCOMBC FrederickHuangLin
24
98
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
71 commits to bugfix branch, last one 5 months ago
david-barnett
microViz david-barnett
10
94
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
865 commits to main branch, last one 22 days ago
cafferychen777
ggpicrust2 cafferychen777
11
91
other
2
Make Picrust2 Output Analysis and Visualization Easier
16s-rrna picrust2 tax4fun2 microbiome microbiota metagenomics visualization functional-data metagenomic-analysis
Created 2022-12-17
273 commits to main branch, last one 2 months ago
pirovc
ganon pirovc
12
83
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 4 months ago
micom-dev
micom micom-dev
17
82
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
784 commits to main branch, last one 10 days ago
MangiolaLaboratory
sccomp MangiolaLaboratory
7
82
unknown
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
1,339 commits to master branch, last one 10 hours ago
MicrobeLab
DeepMicrobes MicrobeLab
21
81
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 about a year ago
microbiome
OMA microbiome
42
75
unknown
11
Orchestrating Microbiome Analysis
r microbiome bioconductor microbiome-analysis-book
Created 2020-11-02
802 commits to devel branch, last one 2 days ago
meringlab
FlashWeave.jl meringlab
8
70
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 24 days ago
zoecastillo
microbiomeExplorer zoecastillo
21
67
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 about a year ago
biocore
gemelli biocore
17
67
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
345 commits to master branch, last one 14 days ago
qiyunzhu
woltka qiyunzhu
24
65
bsd-3-clause
9
Woltka: a versatile meta'omic data classifier
microbiome metagenomics bioinformatics
Created 2020-01-20
497 commits to main branch, last one 3 months ago
SPAAM-community
AncientMetagenomeDir SPAAM-community
30
64
cc-by-4.0
13
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
dataset sedadna metadata pathogen microbiome ancient-dna archaeology metagenomics palaeogenomics metagenomics-data
Created 2020-07-26
10,079 commits to master branch, last one 17 hours ago