bioconductor.org "Microbiome" keyword
miaTime 1.2.0
Microbiome Time Series Analysis2 versions - Latest release: 5 months ago - 9.39 thousand downloads total - 8 stars on GitHub - 1 maintainer
MetaDICT 1.2.0
Microbiome data integration method via shared dictionary learning2 versions - Latest release: 5 months ago - 4.72 thousand downloads total - 5 stars on GitHub - 1 maintainer
FinfoMDS 1.2.0
Multidimensional Scaling with F-ratio for microbiome visualization2 versions - Latest release: 5 months ago - 3.75 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 9.4% on bioconductor.org
11 versions - Latest release: 5 months ago - 53.2 thousand downloads total - 196 stars on GitHub - 1 maintainer
MicrobiotaProcess 1.24.0
A comprehensive R package for managing and analyzing microbiome and other ecological data within ...11 versions - Latest release: 5 months ago - 53.2 thousand downloads total - 196 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
8 versions - Latest release: 5 months ago - 23 dependent packages - 1.17 million downloads total - 1 maintainer
phyloseq 1.56.0
Handling and analysis of high-throughput microbiome census data8 versions - Latest release: 5 months ago - 23 dependent packages - 1.17 million downloads total - 1 maintainer
decontam 1.32.0
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data7 versions - Latest release: 5 months ago - 1 dependent package - 172 thousand downloads total - 176 stars on GitHub - 1 maintainer
Top 7.6% on bioconductor.org
8 versions - Latest release: 5 months ago - 8 dependent packages - 928 thousand downloads total - 8 stars on GitHub - 1 maintainer
biomformat 1.40.0
An interface package for the BIOM file format8 versions - Latest release: 5 months ago - 8 dependent packages - 928 thousand downloads total - 8 stars on GitHub - 1 maintainer
dar 1.8.0
Differential Abundance Analysis by Consensus5 versions - Latest release: 4 months ago - 10.2 thousand downloads total - 7 stars on GitHub - 1 maintainer
omicplotR 1.32.0
Visual Exploration of Omic Datasets Using a Shiny App7 versions - Latest release: 4 months ago - 20.2 thousand downloads total - 1 maintainer
mbQTL 1.12.0
mbQTL: A package for SNP-Taxa mGWAS analysis7 versions - Latest release: 5 months ago - 9.92 thousand downloads total - 1 maintainer
maaslin3 1.4.0
"Refining and extending generalized multivariate linear models for meta-omic association discovery"4 versions - Latest release: 5 months ago - 10.1 thousand downloads total - 1 maintainer
DspikeIn 1.2.0
Estimating Absolute Abundance from Microbial Spike-in Controls3 versions - Latest release: 5 months ago - 9.06 thousand downloads total - 16 stars on GitHub - 1 maintainer
SpiecEasi 2.0.0
Sparse Inverse Covariance for Ecological Statistical Inference1 version - Latest release: 5 months ago - 4.58 thousand downloads total - 234 stars on GitHub - 1 maintainer
CrcBiomeScreen 1.0.0
An R package for colorectal cancer screening and microbiome analysis1 version - Latest release: 5 months ago - 3.32 thousand downloads total - 0 stars on GitHub - 1 maintainer
MicrobiomeProfiler 1.18.1
An R/shiny package for microbiome functional enrichment analysis7 versions - Latest release: 5 months ago - 19.5 thousand downloads total - 42 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
7 versions - Latest release: 5 months ago - 4 dependent packages - 165 thousand downloads total - 31 stars on GitHub - 1 maintainer
ALDEx2 1.44.0
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account7 versions - Latest release: 5 months ago - 4 dependent packages - 165 thousand downloads total - 31 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
8 versions - Latest release: 5 months ago - 7 dependent packages - 250 thousand downloads total - 58 stars on GitHub - 1 maintainer
mia 1.20.0
Microbiome analysis8 versions - Latest release: 5 months ago - 7 dependent packages - 250 thousand downloads total - 58 stars on GitHub - 1 maintainer
microbiomeMarker 1.12.2 removed
microbiome biomarker analysis toolkit7 versions - Latest release: over 1 year ago - 20.2 thousand downloads total - 199 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
9 versions - Latest release: 5 months ago - 3 dependent packages - 171 thousand downloads total - 144 stars on GitHub - 1 maintainer
ANCOMBC 2.14.0
Microbiome differential abudance and correlation analyses with bias correction9 versions - Latest release: 5 months ago - 3 dependent packages - 171 thousand downloads total - 144 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
7 versions - Latest release: 5 months ago - 2 dependent packages - 264 thousand downloads total - 319 stars on GitHub - 1 maintainer
microbiome 1.34.0
Microbiome Analytics7 versions - Latest release: 5 months ago - 2 dependent packages - 264 thousand downloads total - 319 stars on GitHub - 1 maintainer
TaxSEA 1.4.0
Taxon Set Enrichment Analysis3 versions - Latest release: 5 months ago - 9.76 thousand downloads total - 11 stars on GitHub - 1 maintainer
miaDash 1.4.0
Dashboard for the interactive analysis and exploration of microbiome data3 versions - Latest release: 5 months ago - 6.49 thousand downloads total - 1 stars on GitHub - 1 maintainer
metabinR 2.0.0
Abundance and Compositional Based Binning of Metagenomes7 versions - Latest release: 4 months ago - 12.3 thousand downloads total - 2 stars on GitHub - 1 maintainer
combi 1.24.0
Compositional omics model based visual integration7 versions - Latest release: 4 months ago - 17.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
MBECS 1.16.0
Evaluation and correction of batch effects in microbiome data-sets7 versions - Latest release: 4 months ago - 15 thousand downloads total - 4 stars on GitHub - 1 maintainer
MGnifyR 1.8.0
R interface to EBI MGnify metagenomics resource6 versions - Latest release: 4 months ago - 11.2 thousand downloads total - 23 stars on GitHub - 1 maintainer
HoloFoodR 1.6.0
R interface to EBI HoloFood resource4 versions - Latest release: 5 months ago - 7.93 thousand downloads total - 2 stars on GitHub - 1 maintainer
rRDP 1.44.0 removed
Interface to the RDP Classifier6 versions - Latest release: 11 months ago - 22.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
ExpoRiskR 1.0.0
Exposure-Aware Multi-Omics Risk Modeling1 version - Latest release: 5 months ago - 2.95 thousand downloads total - 0 stars on GitHub - 1 maintainer
bugsigdbr 1.18.0
R-side access to published microbial signatures from BugSigDB17 versions - Latest release: 5 months ago - 25.2 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 3.0% on bioconductor.org
8 versions - Latest release: 5 months ago - 11 dependent packages - 272 thousand downloads total - 75 stars on GitHub - 1 maintainer
metagenomeSeq 1.54.0
Statistical analysis for sparse high-throughput sequencing8 versions - Latest release: 5 months ago - 11 dependent packages - 272 thousand downloads total - 75 stars on GitHub - 1 maintainer
iSEEtree 1.6.0
Interactive visualisation for microbiome data4 versions - Latest release: 5 months ago - 8.95 thousand downloads total - 3 stars on GitHub - 1 maintainer
zitools 1.6.0
Analysis of zero-inflated count data4 versions - Latest release: 4 months ago - 7.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
IFAA 1.14.0
Robust Inference for Absolute Abundance in Microbiome Analysis7 versions - Latest release: 5 months ago - 34.5 thousand downloads total - 1 maintainer
philr 1.38.0
Phylogenetic partitioning based ILR transform for metagenomics data7 versions - Latest release: 5 months ago - 40 thousand downloads total - 19 stars on GitHub - 1 maintainer
PathoStat 1.38.0
PathoStat Statistical Microbiome Analysis Package7 versions - Latest release: 5 months ago - 25.7 thousand downloads total - 7 stars on GitHub - 2 maintainers
Top 3.5% on bioconductor.org
7 versions - Latest release: 5 months ago - 2 dependent packages - 941 thousand downloads total - 558 stars on GitHub - 1 maintainer
dada2 1.40.0
Accurate, high-resolution sample inference from amplicon sequencing data7 versions - Latest release: 5 months ago - 2 dependent packages - 941 thousand downloads total - 558 stars on GitHub - 1 maintainer
microbiomeDASim 1.26.0
Microbiome Differential Abundance Simulation7 versions - Latest release: 5 months ago - 14.9 thousand downloads total - 3 stars on GitHub - 1 maintainer
miaViz 1.20.0
Microbiome Analysis Plotting and Visualization8 versions - Latest release: 4 months ago - 2 dependent packages - 31.5 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
7 versions - Latest release: 5 months ago - 5 dependent packages - 583 thousand downloads total - 12 stars on GitHub - 1 maintainer
DirichletMultinomial 1.54.0
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data7 versions - Latest release: 5 months ago - 5 dependent packages - 583 thousand downloads total - 12 stars on GitHub - 1 maintainer
MMUPHin 2.0.0
Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies8 versions - Latest release: 5 months ago - 31.1 thousand downloads total - 1 maintainer
PLSDAbatch 2.0.0
PLSDA-batch5 versions - Latest release: 5 months ago - 10.6 thousand downloads total - 16 stars on GitHub - 1 maintainer
anansi 1.2.0
Annotation-Based Analysis of Specific Interactions2 versions - Latest release: 4 months ago - 8.76 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
8 versions - Latest release: about 2 months ago - 7 dependent packages - 416 thousand downloads total - 1 maintainer
DECIPHER 3.8.1
Tools for curating, analyzing, and manipulating biological sequences8 versions - Latest release: about 2 months ago - 7 dependent packages - 416 thousand downloads total - 1 maintainer
animalcules 1.28.0
Interactive microbiome analysis toolkit10 versions - Latest release: 4 months ago - 34.2 thousand downloads total - 55 stars on GitHub - 1 maintainer
miaSim 1.18.0
Microbiome Data Simulation7 versions - Latest release: 5 months ago - 14.8 thousand downloads total - 22 stars on GitHub - 1 maintainer
CBEA 1.8.0 removed
Competitive Balances for Taxonomic Enrichment Analysis in R5 versions - Latest release: over 1 year ago - 5.49 thousand downloads total - 4 stars on GitHub - 1 maintainer
PERFect 1.16.0 removed
Permutation filtration for microbiome data3 versions - Latest release: almost 3 years ago - 4.92 thousand downloads total - 3 stars on GitHub - 1 maintainer
RCM 1.28.0
Fit row-column association models with the negative binomial distribution for the microbiome7 versions - Latest release: 4 months ago - 23.7 thousand downloads total - 1 maintainer
Rbec 1.20.0
Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities7 versions - Latest release: 4 months ago - 13.7 thousand downloads total - 1 maintainer
OmicsLonDA 1.18.0 removed
Omics Longitudinal Differential Analysis2 versions - Latest release: almost 3 years ago - 5.95 thousand downloads total - 7 stars on GitHub - 1 maintainer
microSTASIS 1.12.0
Microbiota STability ASsessment via Iterative cluStering7 versions - Latest release: 5 months ago - 7.34 thousand downloads total - 1 maintainer
mbOmic 1.6.0 removed
Integrative analysis of the microbiome and metabolome2 versions - Latest release: almost 3 years ago - 896 downloads total - 1 stars on GitHub - 1 maintainer
countsimQC 1.30.0
Compare Characteristic Features of Count Data Sets8 versions - Latest release: 5 months ago - 1 dependent package - 37.3 thousand downloads total - 31 stars on GitHub - 1 maintainer
lefser 1.22.0
R implementation of the LEfSE method for microbiome biomarker discovery9 versions - Latest release: 5 months ago - 1 dependent package - 108 thousand downloads total - 68 stars on GitHub - 1 maintainer
Top 9.0% on bioconductor.org
8 versions - Latest release: 5 months ago - 4 dependent packages - 100 thousand downloads total - 1 maintainer
Maaslin2 1.26.0
"Multivariable Association Discovery in Population-scale Meta-omics Studies"8 versions - Latest release: 5 months ago - 4 dependent packages - 100 thousand downloads total - 1 maintainer
microbiomeExplorer 1.22.0
Microbiome Exploration App7 versions - Latest release: 5 months ago - 23.1 thousand downloads total - 1 maintainer
SIAMCAT 2.16.0
Statistical Inference of Associations between Microbial Communities And host phenoTypes7 versions - Latest release: 5 months ago - 31.1 thousand downloads total - 1 maintainer
ADAPT 1.6.0
Analysis of Microbiome Differential Abundance by Pooling Tobit Models4 versions - Latest release: 4 months ago - 6.01 thousand downloads total - 1 maintainer
reconsi 1.24.0
Resampling Collapsed Null Distributions for Simultaneous Inference7 versions - Latest release: 5 months ago - 14.4 thousand downloads total - 2 stars on GitHub - 1 maintainer
MeLSI 1.0.1
Metric Learning for Statistical Inference in Microbiome Analysis2 versions - Latest release: 2 months ago - 3.08 thousand downloads total - 1 maintainer
benchdamic 1.18.0
Benchmark of differential abundance methods on microbiome data14 versions - Latest release: 4 months ago - 14.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
BDMMAcorrect 1.22.0 removed
Meta-analysis for the metagenomic read counts data from different cohorts3 versions - Latest release: over 2 years ago - 6.75 thousand downloads total - 1 maintainer
sparseDOSSA 1.28.0 removed
Sparse Data Observations for Simulating Synthetic Abundance3 versions - Latest release: over 2 years ago - 8.65 thousand downloads total - 1 maintainer
Related Keywords
Software
64
Metagenomics
33
Sequencing
27
Visualization
20
ImmunoOncology
17
Classification
13
Normalization
12
microbiome
12
MultipleComparison
11
DataImport
11
DifferentialExpression
10
Clustering
9
Regression
6
BatchEffect
5
bioconductor
5
Metabolomics
5
GeneticVariability
5
StatisticalMethod
5
RNASeq
5
Bayesian
5
bioinformatics
4
QualityControl
4
DimensionReduction
4
metagenomics
4
differential-abundance-analysis
3
rstats
3
Transcriptomics
3
microbiome-analysis
3
GeneSetEnrichment
3
r
3
DNASeq
3
Network
3
Preprocessing
3
Infrastructure
3
GUI
3
WholeGenome
2
biomarker-discovery
2
microbiology
2
phyloseq
2
visualisation
2
ShinyApps
2
r-package
2
visualization
2
Coverage
2
SystemsBiology
2
ExperimentalDesign
2
GraphAndNetwork
2
r01ca230551
2
bioconductor-package
2
KEGG
2
GeneExpression
2
Phylogenetics
2
amplicon
2
Microarray
2
metabarcoding
2
ReportWriting
2
Genetics
2
FeatureExtraction
2
MicrobiomeData
2
PrincipalComponent
2
Alignment
2
Posterior p-value
1
lefse
1
Scale simulation
1
taxonomy
1
MicrobialStrain
1
ancom
1
Pathways
1
sequencing
1
PatternLogic
1
SingleCell
1
ancombc
1
NetworkInference
1
absolute-abundances
1
classification
1
amplicon-sequencing
1
gene-copies
1
secom
1
phylogenetic-trees
1
qiime2
1
normalization
1
correlation
1
quantifying
1
ancombc2
1
spike-ins
1
transformation
1
whole-cell
1
SequenceMatching
1
plotting
1
taxonomic-enrichment-analysis
1
enrichment-analysis
1
shiny-apps
1
TimeCourse
1
Survival
1
Proteomics
1
Lipidomics
1
feature-selection
1
FlowCytometry
1
microbiome-data
1
ComparativeGenomics
1