biomformat | cran | Package Usage

microbiome/mia

Microbiome analysis

* DESCRIPTION

Size: 21.1 MB - Last synced: 9 days ago - Pushed: 9 days ago

grunwaldlab/metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

* DESCRIPTION

Size: 108 MB - Last synced: 2 months ago - Pushed: 3 months ago

YuLab-SMU/MicrobiotaProcess

:microbe: A comprehensive R package for deep mining microbiome

* DESCRIPTION

Size: 6.86 MB - Last synced: 17 days ago - Pushed: 18 days ago

KasperSkytte/ampvis2

Tools for visualising microbial community amplicon data

* DESCRIPTION

Size: 132 MB - Last synced: 11 days ago - Pushed: 11 days ago

PLN-team/PLNmodels

A collection of Poisson lognormal models for multivariate count data analysis

* DESCRIPTION

Size: 107 MB - Last synced: 26 days ago - Pushed: 26 days ago

xia-lab/MicrobiomeAnalystR

A companion R package for the MicrobiomeAnalyst web server

* DESCRIPTION

Size: 1.61 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

waldronlab/MicrobiomeBenchmarkDataPrep

Preparation of datasets for MicrobiomeBenchmarkData

* DESCRIPTION

Size: 3.55 MB - Last synced: 10 months ago - Pushed: almost 2 years ago

r-pkg-team/r-bioc-metagenomeseq

r-bioc-metagenomeseq packaging

* DESCRIPTION

Last synced: over 1 year ago

r-pkg-team/r-bioc-phyloseq

r-bioc-phyloseq packaging

>= 1.0.0 DESCRIPTION

Last synced: over 1 year ago

leffj/mctoolsr

Microbial community analysis tools in R

* DESCRIPTION

Size: 5.93 MB - Last synced: 7 months ago - Pushed: almost 2 years ago

HCBravoLab/metagenomeSeq

Statistical analysis for sparse high-throughput sequencing

* DESCRIPTION

Size: 14.2 MB - Last synced: 22 days ago - Pushed: 3 months ago

pooranis/datavis16s

* DESCRIPTION

Last synced: over 1 year ago

HuaZou/MicrobiomeAnalysis

Data analysis and visualization on microbiome data

* DESCRIPTION

Size: 4.17 MB - Last synced: 21 days ago - Pushed: 21 days ago

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

>= 1.0.0 DESCRIPTION

Size: 112 MB - Last synced: 22 days ago - Pushed: about 1 month ago

larssnip/midiv

R code for MiDiv lab

* DESCRIPTION

Size: 77.1 KB - Last synced: 9 months ago - Pushed: 9 months ago

metabaRfactory/metabaR

metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.

* DESCRIPTION

Size: 126 MB - Last synced: 7 months ago - Pushed: over 1 year ago

twbattaglia/btools

A set of R functions that help faciliate a lot of tedious processing

* DESCRIPTION

Size: 497 KB - Last synced: about 2 months ago - Pushed: almost 6 years ago

wejlab/MetaScope

An R-based approach for preprocessing and aligning 16S, metagenomic, and metatranscriptomic data (PathoScope version 3.0)

* DESCRIPTION

Size: 30.2 MB - Last synced: 10 days ago - Pushed: about 1 month ago

yiluheihei/microbiomeMarker

R package for microbiome biomarker discovery

* DESCRIPTION

Size: 23.6 MB - Last synced: 22 days ago - Pushed: 7 months ago

wejlab/animalcules

R shiny app for interactive microbiome analysis

* DESCRIPTION

Size: 18.6 MB - Last synced: 11 days ago - Pushed: 4 months ago

pooranis/dada2nephele

DADA2 16S workflow

* DESCRIPTION

Last synced: over 1 year ago

niaid/nephele2

* pipelines/DADA2/dada2nephele/DESCRIPTION
* pipelines/datavis16s/DESCRIPTION

Size: 10.1 MB - Last synced: 5 months ago - Pushed: almost 2 years ago

pbradz/phylogenize

Repository for phylogenize, a web app to associate microbial genes with microbial prevalence in, and/or specificity to, a given environment.

* package/phylogenize/DESCRIPTION

Size: 26.6 MB - Last synced: over 1 year ago

sysbiobig/metabenchda

metaBenchDA: Investigating Differential Abundance methods in microbiome data: a benchmark study

* DESCRIPTION

Last synced: about 1 year ago

hjfan527/MetaScope Fork of compbiomed/MetaScope

An R-based approach for preprocessing and aligning 16S, metagenomic, and metatranscriptomic data (PathoScope version 3.0)

* DESCRIPTION

Size: 20.1 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

ecastron/phyloseq

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/phyloseq.html Contributions: http://dx.plos.org/10.1371/journal.pone.0061217. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=phyloseq or https://github.com/joey711/phyloseq/issues.

>= 0.4.0 DESCRIPTION

Size: 6.35 MB - Last synced: over 1 year ago - Pushed: about 8 years ago

LisaNicvert/EcoNetwork_public

The public repository with codes I wrote for my Master 2 internship about the inference of co-occurrence networks of large African mammals from camera trap data

* packrat/lib/x86_64-pc-linux-gnu/3.6.2/PLNmodels/DESCRIPTION

Size: 524 MB - Last synced: 7 months ago - Pushed: about 4 years ago

pmartR/pmartRseq

* DESCRIPTION

Size: 286 KB - Last synced: 9 months ago - Pushed: almost 6 years ago

cran/metacoder

:exclamation: This is a read-only mirror of the CRAN R package repository. metacoder — Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data. Homepage: https://grunwaldlab.github.io/metacoder_documentation/ Report bugs for this package: https://github.com/grunwaldlab/metacoder/issues

* DESCRIPTION

Size: 4.54 MB - Last synced: 3 months ago - Pushed: 3 months ago

HCBravoLab/metagenomeSeq-1 Fork of sirusb/metagenomeSeq

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/metagenomeSeq.html Contributions: https://github.com/nosson/metagenomeSeq/. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=metagenomeSeq or https://github.com/nosson/metagenomeSeq/issues.

* DESCRIPTION

Size: 3.48 MB - Last synced: 2 months ago - Pushed: over 8 years ago

kstagaman/microbData

Data Wrangling for Microbiome Analyses

* DESCRIPTION

Size: 883 KB - Last synced: 2 months ago - Pushed: 2 months ago

amcdavid/CoordinatedMicrobiome

Analysis for "Neonatal gut and respiratory microbiota: coordinated development through time and space"

* CoordinatedMBDeps/DESCRIPTION

Size: 8.73 MB - Last synced: about 1 year ago - Pushed: almost 6 years ago

erenada/pipeline_phylogenize-mouse-iMGMC

modified R package "phylogenize" to be run with custom-made mouse focused MIDAS2 database.

* pbradz-phylogenize/package/phylogenize/DESCRIPTION

Size: 19.3 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

ShirleyLiu-BCH/MicrobiomeAnalystR Fork of xia-lab/MicrobiomeAnalystR

A companion R package for the MicrobiomeAnalyst web server

* DESCRIPTION

Size: 1.25 MB - Last synced: 11 months ago - Pushed: about 1 year ago

oloBion/microbiomeExplorer Fork of zoecastillo/microbiomeExplorer

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 N. Paulson.

* DESCRIPTION

Size: 1.82 MB - Last synced: about 1 month ago - Pushed: 11 months ago

GenomicsNX/microbiomeExplorer Fork of zoecastillo/microbiomeExplorer

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 N. Paulson.

* DESCRIPTION

Size: 1.8 MB - Last synced: about 2 months ago - Pushed: over 3 years ago

bioc/mia

This is a read-only mirror of the git repos at https://bioconductor.org

* DESCRIPTION

Size: 11 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

g-antonello/gautils

* DESCRIPTION

Size: 7.99 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

diegoibt/phyloseq Fork of joey711/phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

>= 1.0.0 DESCRIPTION

Size: 111 MB - Last synced: 10 months ago - Pushed: about 5 years ago

rvarki/MetaScope Fork of compbiomed/MetaScope

An R-based approach for preprocessing and aligning 16S, metagenomic, and metatranscriptomic data (PathoScope version 3.0)

* DESCRIPTION

Size: 20.1 MB - Last synced: 10 months ago - Pushed: over 2 years ago

Wellington9023/microbiomeMarker Fork of yiluheihei/microbiomeMarker

R package for microbiome biomarker discovery

* DESCRIPTION

Size: 14.8 MB - Last synced: 9 months ago - Pushed: 9 months ago

Wellington9023/phyloseq Fork of joey711/phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

>= 1.0.0 DESCRIPTION

Size: 112 MB - Last synced: 9 months ago - Pushed: about 4 years ago

YinsuW/microbiomeExplorer Fork of zoecastillo/microbiomeExplorer

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 N. Paulson.

* DESCRIPTION

Size: 1.82 MB - Last synced: 9 months ago - Pushed: over 1 year ago

gavieira/phyloseq Fork of joey711/phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page: