Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "Metagenomics" keyword
microbiomeExplorer 1.12.0
Microbiome Exploration App3 versions - Latest release: 6 months ago - 6.29 thousand downloads total - 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
ccrepe 1.38.1
ccrepe_and_nc.score4 versions - Latest release: 3 months ago - 20.6 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
coRdon 1.20.0
Codon Usage Analysis and Prediction of Gene Expressivity3 versions - Latest release: 6 months ago - 13 thousand downloads total - 17 stars on GitHub - 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
banocc 1.26.0
Bayesian ANalysis Of Compositional Covariance3 versions - Latest release: 6 months ago - 9.88 thousand downloads total - 2 maintainers
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
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
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 2.6% on bioconductor.org
3 versions - Latest release: 13 days ago - 9 dependent packages - 214 thousand downloads total - 1 maintainer
mixOmics 6.28.0
Omics Data Integration Project3 versions - Latest release: 13 days ago - 9 dependent packages - 214 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
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 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
timeOmics 1.16.0
Time-Course Multi-Omics data integration3 versions - Latest release: 13 days ago - 1 dependent package - 5.04 thousand downloads total - 21 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 2.7% 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
fastreeR 1.8.0
Phylogenetic, Distance and Other Calculations on VCF and Fasta Files3 versions - Latest release: 15 days ago - 2.61 thousand downloads total - 1 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
MGnifyR 1.0.0
R interface to EBI MGnify metagenomics resource1 version - Latest release: 21 days ago - 152 downloads total - 16 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
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
OGRE 1.6.0
Calculate, visualize and analyse overlap between genomic regions2 versions - Latest release: 6 months ago - 1.77 thousand downloads total - 2 stars on GitHub - 1 maintainer
metavizr 1.24.0 removed
R Interface to the metaviz web app for interactive metagenomics data analysis and visualization1 version - Latest release: 7 months ago - 7.94 thousand downloads total - 1 maintainer
Related Keywords
Software
36
Microbiome
27
ImmunoOncology
19
Sequencing
17
Classification
10
Visualization
10
MultipleComparison
9
Clustering
7
DifferentialExpression
6
Normalization
5
microbiome
5
DataImport
4
Regression
4
metagenomics
4
Bayesian
4
GeneticVariability
4
Metabolomics
3
GeneExpression
3
RNASeq
3
Microarray
3
r
3
GenePrediction
3
GeneSetEnrichment
3
DimensionReduction
3
Proteomics
2
amplicon
2
bioinformatics
2
metabarcoding
2
r-package
2
Infrastructure
2
Preprocessing
2
FeatureExtraction
2
Transcriptomics
2
GUI
2
DNASeq
2
integration
1
cluster
1
TimeCourse
1
FlowCytometry
1
multi-omics
1
time-series
1
Scale simulation
1
benchmark
1
differential-abundance-methods
1
biomarker-discovery
1
differential-abundance-analysis
1
lefse
1
bioconductor
1
taxonomy
1
Phylogenetics
1
bioconductor-package
1
Coverage
1
contamination
1
Annotation
1
BiologicalQuestion
1
WorkflowStep
1
Bioinformatics
1
Statistics
1
BiomedicalInformatics
1
Genetics CellBiology
1
KEGG
1
Pathways
1
enrichment-analysis
1
rstats
1
taxonomic-enrichment-analysis
1
GraphAndNetwork
1
PatternLogic
1
PrincipalComponent
1
SNP
1
StatisticalMethod
1
WholeGenome
1
BatchEffect
1
SystemsBiology
1
hitchip
1
hitchip-atlas
1
human-microbiome
1
microbiology
1
microbiome-analysis
1
phyloseq
1
population-study
1
ChIPSeq
1
Posterior p-value
1