Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "Microbiome" keyword
microbiomeExplorer 1.12.0
Microbiome Exploration App3 versions - Latest release: 6 months ago - 6.29 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
3 versions - Latest release: 20 days ago - 7 dependent packages - 49.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
mia 1.12.0
Microbiome analysis3 versions - Latest release: 20 days ago - 7 dependent packages - 49.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
RCM 1.18.0
Fit row-column association models with the negative binomial distribution for the microbiome3 versions - Latest release: 6 months ago - 5.89 thousand downloads total - 1 maintainer
sparseDOSSA 1.26.0
Sparse Data Observations for Simulating Synthetic Abundance3 versions - Latest release: 6 months ago - 8.14 thousand downloads total - 1 maintainer
combi 1.14.0
Compositional omics model based visual integration3 versions - Latest release: 6 months ago - 4.47 thousand downloads total - 0 stars on GitHub - 1 maintainer
omicplotR 1.22.0
Visual Exploration of Omic Datasets Using a Shiny App3 versions - Latest release: 6 months ago - 8.13 thousand downloads total - 1 maintainer
SIAMCAT 2.6.0
Statistical Inference of Associations between Microbial Communities And host phenoTypes3 versions - Latest release: 6 months ago - 11.8 thousand downloads total - 1 maintainer
BDMMAcorrect 1.20.0
Meta-analysis for the metagenomic read counts data from different cohorts3 versions - Latest release: 6 months ago - 6.33 thousand downloads total - 1 maintainer
IFAA 1.4.0
Robust Inference for Absolute Abundance in Microbiome Analysis3 versions - Latest release: 6 months ago - 1.54 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
3 versions - Latest release: 6 months ago - 4 dependent packages - 38.9 thousand downloads total - 1 maintainer
Maaslin2 1.16.0
"Multivariable Association Discovery in Population-scale Meta-omics Studies"3 versions - Latest release: 6 months ago - 4 dependent packages - 38.9 thousand downloads total - 1 maintainer
miaViz 1.10.0
Microbiome Analysis Plotting and Visualization3 versions - Latest release: 6 months ago - 2 dependent packages - 8.83 thousand downloads total - 1 maintainer
CBEA 1.3.0
Competitive Balances for Taxonomic Enrichment Analysis in R3 versions - Latest release: 7 months ago - 2.75 thousand downloads total - 5 stars on GitHub - 1 maintainer
PathoStat 1.28.0
PathoStat Statistical Microbiome Analysis Package3 versions - Latest release: 6 months ago - 11.4 thousand downloads total - 8 stars on GitHub - 2 maintainers
rRDP 1.36.0
Interface to the RDP Classifier3 versions - Latest release: 6 months ago - 14.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
Rbec 1.10.0
Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities3 versions - Latest release: 6 months ago - 2.62 thousand downloads total - 1 maintainer
mbOmic 1.6.0 removed
Integrative analysis of the microbiome and metabolome2 versions - Latest release: 6 months ago - 896 downloads total - 0 stars on GitHub - 1 maintainer
mbQTL 1.2.0
mbQTL: A package for SNP-Taxa mGWAS analysis3 versions - Latest release: 6 months ago - 1.26 thousand downloads total - 1 maintainer
microSTASIS 1.2.0
Microbiota STability ASsessment via Iterative cluStering3 versions - Latest release: 6 months ago - 1.44 thousand downloads total - 1 maintainer
MMUPHin 1.16.0
Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies3 versions - Latest release: 6 months ago - 7.52 thousand downloads total - 1 maintainer
countsimQC 1.22.0
Compare Characteristic Features of Count Data Sets3 versions - Latest release: 20 days ago - 1 dependent package - 9 thousand downloads total - 27 stars on GitHub - 1 maintainer
MicrobiomeProfiler 1.10.0
An R/shiny package for microbiome functional enrichment analysis3 versions - Latest release: 7 days ago - 3.56 thousand downloads total - 33 stars on GitHub - 1 maintainer
Top 9.4% on bioconductor.org
4 versions - Latest release: 10 days ago - 20.1 thousand downloads total - 160 stars on GitHub - 1 maintainer
MicrobiotaProcess 1.16.0
A comprehensive R package for managing and analyzing microbiome and other ecological data within ...4 versions - Latest release: 10 days ago - 20.1 thousand downloads total - 160 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
2 versions - Latest release: 7 months ago - 23 dependent packages - 687 thousand downloads total - 1 maintainer
phyloseq 1.46.0
Handling and analysis of high-throughput microbiome census data2 versions - Latest release: 7 months ago - 23 dependent packages - 687 thousand downloads total - 1 maintainer
Top 2.4% on bioconductor.org
2 versions - Latest release: 6 months ago - 2 dependent packages - 113 thousand downloads total - 270 stars on GitHub - 1 maintainer
microbiome 1.24.0
Microbiome Analytics2 versions - Latest release: 6 months ago - 2 dependent packages - 113 thousand downloads total - 270 stars on GitHub - 1 maintainer
Top 3.0% on bioconductor.org
3 versions - Latest release: 13 days ago - 11 dependent packages - 148 thousand downloads total - 62 stars on GitHub - 1 maintainer
metagenomeSeq 1.46.0
Statistical analysis for sparse high-throughput sequencing3 versions - Latest release: 13 days ago - 11 dependent packages - 148 thousand downloads total - 62 stars on GitHub - 1 maintainer
lefser 1.14.0
R implementation of the LEfSE method for microbiome biomarker discovery4 versions - Latest release: 20 days ago - 1 dependent package - 16.8 thousand downloads total - 31 stars on GitHub - 1 maintainer
Top 7.6% on bioconductor.org
3 versions - Latest release: 13 days ago - 8 dependent packages - 479 thousand downloads total - 7 stars on GitHub - 1 maintainer
biomformat 1.32.0
An interface package for the BIOM file format3 versions - Latest release: 13 days ago - 8 dependent packages - 479 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
3 versions - Latest release: 17 days ago - 3 dependent packages - 50.4 thousand downloads total - 89 stars on GitHub - 1 maintainer
ANCOMBC 2.6.0
Microbiome differential abudance and correlation analyses with bias correction3 versions - Latest release: 17 days ago - 3 dependent packages - 50.4 thousand downloads total - 89 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
3 versions - Latest release: 13 days ago - 4 dependent packages - 75.9 thousand downloads total - 24 stars on GitHub - 1 maintainer
ALDEx2 1.36.0
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account3 versions - Latest release: 13 days ago - 4 dependent packages - 75.9 thousand downloads total - 24 stars on GitHub - 1 maintainer
reconsi 1.16.0
Resampling Collapsed Null Distributions for Simultaneous Inference3 versions - Latest release: 11 days ago - 3.89 thousand downloads total - 2 stars on GitHub - 1 maintainer
benchdamic 1.10.0
Benchmark of differential abundance methods on microbiome data5 versions - Latest release: 13 days ago - 3.07 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
3 versions - Latest release: 13 days ago - 7 dependent packages - 208 thousand downloads total - 1 maintainer
DECIPHER 3.0.0
Tools for curating, analyzing, and manipulating biological sequences3 versions - Latest release: 13 days ago - 7 dependent packages - 208 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
3 versions - Latest release: 13 days ago - 5 dependent packages - 267 thousand downloads total - 1 maintainer
DirichletMultinomial 1.46.0
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data3 versions - Latest release: 13 days ago - 5 dependent packages - 267 thousand downloads total - 1 maintainer
microbiomeMarker 1.10.0
microbiome biomarker analysis toolkit4 versions - Latest release: 13 days ago - 13.5 thousand downloads total - 160 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
3 versions - Latest release: 15 days ago - 2 dependent packages - 727 thousand downloads total - 446 stars on GitHub - 1 maintainer
dada2 1.32.0
Accurate, high-resolution sample inference from amplicon sequencing data3 versions - Latest release: 15 days ago - 2 dependent packages - 727 thousand downloads total - 446 stars on GitHub - 1 maintainer
metabinR 1.6.0
Abundance and Compositional Based Binning of Metagenomes3 versions - Latest release: 16 days ago - 1.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
bugsigdbr 1.10.0
R-side access to published microbial signatures from BugSigDB6 versions - Latest release: 20 days ago - 4.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
PLSDAbatch 1.0.0
PLSDA-batch1 version - Latest release: 21 days ago - 186 downloads total - 10 stars on GitHub - 1 maintainer
dar 1.0.0
Differential Abundance Analysis by Consensus1 version - Latest release: 21 days ago - 145 downloads total - 1 stars on GitHub - 1 maintainer
philr 1.28.0
Phylogenetic partitioning based ILR transform for metagenomics data2 versions - Latest release: 6 months ago - 19.9 thousand downloads total - 19 stars on GitHub - 1 maintainer
animalcules 1.18.3
Interactive microbiome analysis toolkit4 versions - Latest release: 3 months ago - 8.28 thousand downloads total - 51 stars on GitHub - 1 maintainer
PERFect 1.16.0
Permutation filtration for microbiome data2 versions - Latest release: 6 months ago - 4.61 thousand downloads total - 2 stars on GitHub - 1 maintainer
miaSim 1.8.0
Microbiome Data Simulation2 versions - Latest release: 6 months ago - 3.06 thousand downloads total - 15 stars on GitHub - 1 maintainer
microbiomeDASim 1.16.0
Microbiome Differential Abundance Simulation2 versions - Latest release: 6 months ago - 4.54 thousand downloads total - 3 stars on GitHub - 1 maintainer
decontam 1.22.0
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data2 versions - Latest release: 6 months ago - 1 dependent package - 56.6 thousand downloads total - 131 stars on GitHub - 1 maintainer
MBECS 1.6.0
Evaluation and correction of batch effects in microbiome data-sets2 versions - Latest release: 6 months ago - 2.13 thousand downloads total - 4 stars on GitHub - 1 maintainer
OmicsLonDA 1.18.0
Omics Longitudinal Differential Analysis2 versions - Latest release: 6 months ago - 5.95 thousand downloads total - 5 stars on GitHub - 1 maintainer
Related Keywords
Software
47
Metagenomics
27
Sequencing
22
ImmunoOncology
17
Visualization
15
Classification
12
MultipleComparison
9
Clustering
8
DifferentialExpression
8
microbiome
8
Normalization
8
DataImport
6
GeneticVariability
5
Bayesian
5
BatchEffect
4
Regression
4
metagenomics
4
RNASeq
4
r
3
QualityControl
3
StatisticalMethod
3
Transcriptomics
3
DNASeq
3
Metabolomics
3
DimensionReduction
3
Network
2
Genetics
2
WholeGenome
2
Alignment
2
Preprocessing
2
ReportWriting
2
microbiome-analysis
2
bioconductor-package
2
differential-abundance-analysis
2
amplicon
2
bioinformatics
2
metabarcoding
2
Coverage
2
FeatureExtraction
2
GeneSetEnrichment
2
GeneExpression
2
r-package
2
bioconductor
2
rstats
2
PrincipalComponent
2
Microarray
2
normalization
1
secom
1
sequencing
1
ChIPSeq
1
Posterior p-value
1
Scale simulation
1
FlowCytometry
1
benchmark
1
differential-abundance-methods
1
TimeCourse
1
GenePrediction
1
qPCR
1
biomarker-discovery
1
lefse
1
Survival
1
GUI
1
Proteomics
1
Lipidomics
1
taxonomy
1
contamination
1
analysis
1
ATACSeq
1
PatternLogic
1
Infrastructure
1
SequenceMatching
1
MicrobialStrain
1
GraphAndNetwork
1
SNP
1
taxonomic-enrichment-analysis
1
BiomedicalInformatics
1
ExperimentalDesign
1
enrichment-analysis
1
SingleCell
1
KEGG
1
microbiome-data
1
SystemsBiology
1
hitchip
1
hitchip-atlas
1
human-microbiome
1
microbiology
1
phyloseq
1
population-study
1
Technology
1
ancom
1
ancombc
1
ancombc2
1
correlation
1