bioconductor.org "Microbiome" keyword
View the packages on the bioconductor.org package registry that are tagged with the "Microbiome" keyword.
dar 1.4.0
Differential Abundance Analysis by Consensus3 versions - Latest release: 3 months ago - 3.24 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 9.4% on bioconductor.org
8 versions - Latest release: 2 months ago - 31.4 thousand downloads total - 187 stars on GitHub - 1 maintainer
MicrobiotaProcess 1.20.1
A comprehensive R package for managing and analyzing microbiome and other ecological data within ...8 versions - Latest release: 2 months ago - 31.4 thousand downloads total - 187 stars on GitHub - 1 maintainer
miaDash 1.0.0
Shiny app for the interactive analysis and exploration of microbiome data1 version - Latest release: 3 months ago - 1.14 thousand downloads total - 1 stars on GitHub - 1 maintainer
microbiomeDASim 1.22.0
Microbiome Differential Abundance Simulation5 versions - Latest release: 2 months ago - 8.85 thousand downloads total - 3 stars on GitHub - 1 maintainer
MicrobiomeProfiler 1.14.0
An R/shiny package for microbiome functional enrichment analysis5 versions - Latest release: 3 months ago - 8.48 thousand downloads total - 37 stars on GitHub - 1 maintainer
lefser 1.18.0
R implementation of the LEfSE method for microbiome biomarker discovery7 versions - Latest release: 3 months ago - 1 dependent package - 34 thousand downloads total - 42 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
5 versions - Latest release: 2 months ago - 23 dependent packages - 831 thousand downloads total - 1 maintainer
phyloseq 1.52.0
Handling and analysis of high-throughput microbiome census data5 versions - Latest release: 2 months ago - 23 dependent packages - 831 thousand downloads total - 1 maintainer
philr 1.34.0
Phylogenetic partitioning based ILR transform for metagenomics data5 versions - Latest release: 2 months ago - 25.9 thousand downloads total - 19 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
5 versions - Latest release: 2 months ago - 7 dependent packages - 272 thousand downloads total - 1 maintainer
DECIPHER 3.4.0
Tools for curating, analyzing, and manipulating biological sequences5 versions - Latest release: 2 months ago - 7 dependent packages - 272 thousand downloads total - 1 maintainer
iSEEtree 1.2.0
Interactive visualisation for microbiome data2 versions - Latest release: 3 months ago - 2.69 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 5 dependent packages - 396 thousand downloads total - 11 stars on GitHub - 1 maintainer
DirichletMultinomial 1.50.0
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data5 versions - Latest release: 3 months ago - 5 dependent packages - 396 thousand downloads total - 11 stars on GitHub - 1 maintainer
decontam 1.28.0
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data5 versions - Latest release: 3 months ago - 1 dependent package - 92.7 thousand downloads total - 158 stars on GitHub - 1 maintainer
miaViz 1.16.0
Microbiome Analysis Plotting and Visualization5 versions - Latest release: 3 months ago - 2 dependent packages - 17.5 thousand downloads total - 11 stars on GitHub - 1 maintainer
maaslin3 1.0.0
"Refining and extending generalized multivariate linear models for meta-omic association discovery"1 version - Latest release: 3 months ago - 2.09 thousand downloads total - 1 maintainer
HoloFoodR 1.2.0
R interface to EBI HoloFood resource2 versions - Latest release: 3 months ago - 2.13 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
6 versions - Latest release: 9 days ago - 7 dependent packages - 89.4 thousand downloads total - 52 stars on GitHub - 1 maintainer
mia 1.16.1
Microbiome analysis6 versions - Latest release: 9 days ago - 7 dependent packages - 89.4 thousand downloads total - 52 stars on GitHub - 1 maintainer
ADAPT 1.2.0
Analysis of Microbiome Differential Abundance by Pooling Tobit Models2 versions - Latest release: 3 months ago - 1.23 thousand downloads total - 1 maintainer
miaSim 1.14.0
Microbiome Data Simulation5 versions - Latest release: 3 months ago - 7.38 thousand downloads total - 22 stars on GitHub - 1 maintainer
countsimQC 1.26.0
Compare Characteristic Features of Count Data Sets5 versions - Latest release: 2 months ago - 1 dependent package - 15.8 thousand downloads total - 28 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
5 versions - Latest release: 3 months ago - 2 dependent packages - 791 thousand downloads total - 502 stars on GitHub - 1 maintainer
dada2 1.36.0
Accurate, high-resolution sample inference from amplicon sequencing data5 versions - Latest release: 3 months ago - 2 dependent packages - 791 thousand downloads total - 502 stars on GitHub - 1 maintainer
TaxSEA 1.0.0
Taxon Set Enrichment Analysis1 version - Latest release: 3 months ago - 934 downloads total - 6 stars on GitHub - 1 maintainer
rRDP 1.42.0
Interface to the RDP Classifier5 versions - Latest release: 3 months ago - 18.9 thousand downloads total - 3 stars on GitHub - 1 maintainer
IFAA 1.10.0
Robust Inference for Absolute Abundance in Microbiome Analysis5 versions - Latest release: 3 months ago - 8.65 thousand downloads total - 1 maintainer
zitools 1.2.0
Analysis of zero-inflated count data2 versions - Latest release: 3 months ago - 1.71 thousand downloads total - 0 stars on GitHub - 1 maintainer
animalcules 1.24.0
Interactive microbiome analysis toolkit7 versions - Latest release: 3 months ago - 17.1 thousand downloads total - 55 stars on GitHub - 1 maintainer
bugsigdbr 1.14.3
R-side access to published microbial signatures from BugSigDB13 versions - Latest release: 24 days ago - 12.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
mbQTL 1.8.0
mbQTL: A package for SNP-Taxa mGWAS analysis5 versions - Latest release: 3 months ago - 4.37 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
5 versions - Latest release: 3 months ago - 8 dependent packages - 611 thousand downloads total - 7 stars on GitHub - 1 maintainer
biomformat 1.36.0
An interface package for the BIOM file format5 versions - Latest release: 3 months ago - 8 dependent packages - 611 thousand downloads total - 7 stars on GitHub - 1 maintainer
PLSDAbatch 1.4.0
PLSDA-batch3 versions - Latest release: 3 months ago - 3.7 thousand downloads total - 13 stars on GitHub - 1 maintainer
Rbec 1.16.0
Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities5 versions - Latest release: 3 months ago - 5.94 thousand downloads total - 1 maintainer
PathoStat 1.34.0
PathoStat Statistical Microbiome Analysis Package5 versions - Latest release: 3 months ago - 16.5 thousand downloads total - 8 stars on GitHub - 2 maintainers
MMUPHin 1.22.0
Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies5 versions - Latest release: 3 months ago - 14.8 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 4 dependent packages - 59.1 thousand downloads total - 1 maintainer
Maaslin2 1.22.0
"Multivariable Association Discovery in Population-scale Meta-omics Studies"5 versions - Latest release: 3 months ago - 4 dependent packages - 59.1 thousand downloads total - 1 maintainer
SIAMCAT 2.12.0
Statistical Inference of Associations between Microbial Communities And host phenoTypes5 versions - Latest release: 3 months ago - 16.7 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 4 dependent packages - 105 thousand downloads total - 28 stars on GitHub - 1 maintainer
ALDEx2 1.40.0
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account5 versions - Latest release: 3 months ago - 4 dependent packages - 105 thousand downloads total - 28 stars on GitHub - 1 maintainer
combi 1.20.0
Compositional omics model based visual integration5 versions - Latest release: 3 months ago - 8.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
RCM 1.24.0
Fit row-column association models with the negative binomial distribution for the microbiome5 versions - Latest release: 3 months ago - 9.76 thousand downloads total - 1 maintainer
microSTASIS 1.8.0
Microbiota STability ASsessment via Iterative cluStering5 versions - Latest release: 3 months ago - 4.6 thousand downloads total - 1 maintainer
CBEA 1.8.0
Competitive Balances for Taxonomic Enrichment Analysis in R5 versions - Latest release: 3 months ago - 5.33 thousand downloads total - 6 stars on GitHub - 1 maintainer
MBECS 1.12.0
Evaluation and correction of batch effects in microbiome data-sets5 versions - Latest release: 3 months ago - 7.57 thousand downloads total - 4 stars on GitHub - 1 maintainer
metabinR 1.10.0
Abundance and Compositional Based Binning of Metagenomes5 versions - Latest release: 3 months ago - 4.88 thousand downloads total - 0 stars on GitHub - 1 maintainer
MGnifyR 1.4.0
R interface to EBI MGnify metagenomics resource3 versions - Latest release: 3 months ago - 3.91 thousand downloads total - 21 stars on GitHub - 1 maintainer
benchdamic 1.14.2
Benchmark of differential abundance methods on microbiome data10 versions - Latest release: about 2 months ago - 6.52 thousand downloads total - 5 stars on GitHub - 1 maintainer
microbiomeExplorer 1.18.0
Microbiome Exploration App5 versions - Latest release: 3 months ago - 11.3 thousand downloads total - 1 maintainer
omicplotR 1.28.0
Visual Exploration of Omic Datasets Using a Shiny App5 versions - Latest release: 3 months ago - 12.6 thousand downloads total - 1 maintainer
Top 3.0% on bioconductor.org
6 versions - Latest release: 3 months ago - 11 dependent packages - 185 thousand downloads total - 69 stars on GitHub - 1 maintainer
metagenomeSeq 1.50.0
Statistical analysis for sparse high-throughput sequencing6 versions - Latest release: 3 months ago - 11 dependent packages - 185 thousand downloads total - 69 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
7 versions - Latest release: about 1 month ago - 3 dependent packages - 84.9 thousand downloads total - 122 stars on GitHub - 1 maintainer
ANCOMBC 2.10.1
Microbiome differential abudance and correlation analyses with bias correction7 versions - Latest release: about 1 month ago - 3 dependent packages - 84.9 thousand downloads total - 122 stars on GitHub - 1 maintainer
reconsi 1.20.0
Resampling Collapsed Null Distributions for Simultaneous Inference5 versions - Latest release: 3 months ago - 7.16 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 2 dependent packages - 158 thousand downloads total - 299 stars on GitHub - 1 maintainer
microbiome 1.30.0
Microbiome Analytics5 versions - Latest release: 3 months ago - 2 dependent packages - 158 thousand downloads total - 299 stars on GitHub - 1 maintainer
microbiomeMarker 1.12.2 removed
microbiome biomarker analysis toolkit7 versions - Latest release: 4 months ago - 20.2 thousand downloads total - 173 stars on GitHub - 1 maintainer
BDMMAcorrect 1.22.0 removed
Meta-analysis for the metagenomic read counts data from different cohorts3 versions - Latest release: about 1 year ago - 6.75 thousand downloads total - 1 maintainer
sparseDOSSA 1.28.0 removed
Sparse Data Observations for Simulating Synthetic Abundance3 versions - Latest release: about 1 year ago - 8.65 thousand downloads total - 1 maintainer
OmicsLonDA 1.18.0 removed
Omics Longitudinal Differential Analysis2 versions - Latest release: over 1 year ago - 5.95 thousand downloads total - 5 stars on GitHub - 1 maintainer
mbOmic 1.6.0 removed
Integrative analysis of the microbiome and metabolome2 versions - Latest release: over 1 year ago - 896 downloads total - 0 stars on GitHub - 1 maintainer
PERFect 1.16.0 removed
Permutation filtration for microbiome data3 versions - Latest release: over 1 year ago - 4.92 thousand downloads total - 2 stars on GitHub - 1 maintainer
Related Keywords
Software
55
Metagenomics
31
Sequencing
24
Visualization
17
ImmunoOncology
17
Classification
12
microbiome
12
MultipleComparison
11
Normalization
10
DataImport
10
DifferentialExpression
9
Clustering
8
GeneticVariability
5
bioconductor
5
RNASeq
5
Bayesian
5
StatisticalMethod
4
metagenomics
4
bioinformatics
4
BatchEffect
4
Regression
4
DNASeq
3
Infrastructure
3
QualityControl
3
GeneSetEnrichment
3
differential-abundance-analysis
3
r
3
Metabolomics
3
Transcriptomics
3
rstats
3
microbiome-analysis
3
GUI
3
DimensionReduction
3
Preprocessing
2
GeneExpression
2
Network
2
PrincipalComponent
2
Coverage
2
MicrobiomeData
2
ReportWriting
2
r-package
2
metabarcoding
2
amplicon
2
FeatureExtraction
2
WholeGenome
2
Microarray
2
phyloseq
2
microbiology
2
Genetics
2
ShinyApps
2
Alignment
2
bioconductor-package
2
biomarker-discovery
2
visualisation
2
ancombc2
1
ancombc
1
ancom
1
differential-abundance-methods
1
benchmark
1
taxonomic-enrichment-analysis
1
feature-selection
1
enrichment-analysis
1
BiomedicalInformatics
1
Scale simulation
1
shiny-apps
1
correlation
1
normalization
1
secom
1
sequencing
1
FlowCytometry
1
SystemsBiology
1
hitchip
1
hitchip-atlas
1
human-microbiome
1
population-study
1
lefse
1
Lipidomics
1
Proteomics
1
Survival
1
TimeCourse
1
qPCR
1
contamination
1
plotting
1
visualization
1
GenePrediction
1
analysis
1
ATACSeq
1
KEGG
1
ExperimentalDesign
1
webapp
1
SingleCell
1
taxonomy
1
shiny
1
mia
1
SequenceMatching
1
classification
1
isee
1
Technology
1
r01ca230551
1
SNP
1