diff --git a/inst/assets/_book.yml b/inst/assets/_book.yml index b77f8962..d5ddf328 100644 --- a/inst/assets/_book.yml +++ b/inst/assets/_book.yml @@ -69,6 +69,7 @@ book: - pages/contributions.qmd appendices: - pages/phyloseq_cheatsheet.qmd + - pages/tool_list.qmd - pages/example_solutions.qmd - pages/session_info.qmd favicon: assets/favicon.png diff --git a/inst/pages/contributions.qmd b/inst/pages/contributions.qmd index d403e481..c320a5d5 100644 --- a/inst/pages/contributions.qmd +++ b/inst/pages/contributions.qmd @@ -51,8 +51,7 @@ Julia language, implementing `r BiocStyle::Githubpkg("JuliaTurkuDataScience/MicrobiomeAnalysis.jl")`. - *Sudarshan Shetty, PhD* has supported the establishment of the -framework and associated tools. He also maintains a list of -[microbiome R packages](https://microsud.github.io/Tools-Microbiome-Analysis/). +framework and associated tools. - *Henrik Eckermann* contributed in particular to the development of differential abundance analyses. diff --git a/inst/pages/tool_list.qmd b/inst/pages/tool_list.qmd new file mode 100644 index 00000000..d3df03ad --- /dev/null +++ b/inst/pages/tool_list.qmd @@ -0,0 +1,165 @@ +# Tools for microbiome analysis {#sec-tool_list} + +> A + +Adaptive gPCA [A method for structured dimensionality reduction](https://arxiv.org/abs/1702.00501) +Ampvis2 [Tools for visualising amplicon sequencing data](https://madsalbertsen.github.io/ampvis2/) +ANCOM/ANCOM-BC [R package for Analysis of Composition of Microbiomes (ANCOM-BC)](https://github.com/FrederickHuangLin/ANCOMBC) +animalcules [R shiny app for interactive microbiome analysis](https://compbiomed.github.io/animalcules-docs/) +ALDEx2 [Analysis Of Differential Abundance Taking Sample Variation Into Account](https://bioconductor.org/packages/release/bioc/html/ALDEx2.html) + +> B + +BDMMA [Batch Effects Correction for Microbiome Data With Dirichlet-multinomial Regression](https://academic.oup.com/bioinformatics/article-abstract/35/5/807/5078473) +BEEM [BEEM: Estimating Lotka-Volterra models from time-course microbiome sequencing data](https://github.com/lch14forever/BEEM) +biome-shiny [GUI for microbiome visualization, based on the shiny package "microbiome"](https://github.com/Biodata-PT/Biome-Shiny) +bootLong [The Block Bootstrap Method for Longitudinal Microbiome Data](https://pratheepaj.github.io/bootLong/) +breakaway [Species Richness Estimation and Modeling](https://github.com/search?q=breakaway) + +> C + +CCREPE [Compositionality Corrected by PErmutation and REnormalization](http://bioconductor.org/packages/release/bioc/html/ccrepe.html) +corncob [Modeling microbial abundances and dysbiosis with beta-binomial regression](https://arxiv.org/abs/1902.02776) +curatedMetagenomicData [Accessible, curated metagenomic data through ExperimentHub](https://waldronlab.io/curatedMetagenomicData/) +CoDaSeq [Functions for compositional analysis of high throughput sequencing](https://github.com/ggloor/CoDaSeq) + +> D + +dacomp [Testing for Differential Abundance in Compositional Counts Data, with Application to Microbiome Studies](https://github.com/barakbri/dacomp) +DADA2 [Divisive Amplicon Denoising Algorithm](https://www.nature.com/nmeth/journal/v13/n7/full/nmeth.3869.html) +DECIPHER [Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R](http://www2.decipher.codes/index.html) +DECIPHER/IIDTAXA [IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences](doi:10.1186/s40168-018-0521-5) +decontam [Simple Statistical Identification and Removal of Contaminant Sequences in Marker-Gene and Metagenomics Data](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0605-2) +DESeq2 [Differential expression analysis for sequence count data](https://www.bioconductor.org/packages/devel/bioc/vignettes/phyloseq/inst/doc/phyloseq-mixture-models.html) +diffTop [Differential topic analysis](https://pratheepaj.github.io/diffTop/) +DivNet [An R package to estimate diversity when taxa in the community cooccur via a ecological network](https://github.com/adw96/DivNet) +DMBC [A Dirichlet-Multinomial Bayes Classifier for Disease Diagnosis With Microbial Compositions](https://msphere.asm.org/content/2/6/e00536-17) + +> E + +edgeR [empirical analysis of DGE in R](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/) + +> F + +> G + +GLMMMiRKAT [A distance-based kernel association test based on the generalized linear mixed model](https://github.com/hk1785/GLMM-MiRKAT) + +> H + +> I + +igraph [Network Analysis and Visualization in R](http://igraph.org/r/) + +> J + +> K + +> L + +labdsv [Ordination and Multivariate Analysis for Ecology](https://cran.r-project.org/web/packages/labdsv/labdsv.pdf) + +> M + +MaAsLin2 [MaAsLin2: Microbiome Multivariate Association with Linear Models](https://github.com/biobakery/Maaslin2) +mare [Microbiota Analysis in R Easily](https://github.com/katrikorpela/mare) +massMap [A Two-Stage Microbial Association Mapping Framework With Advanced FDR Control](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0517-1) +mbtools [Collection of R tools to analyze microbiome data](https://gibbons-lab.github.io/mbtools) +MDiNE [MDiNE: a model to estimate differential co-occurrence networks in microbiome studies](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz824/5614428) +MDPbiome [MDPbiome: microbiome engineering through prescriptive perturbations](https://academic.oup.com/bioinformatics/article/34/17/i838/5093255) +microDecon [An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing](https://github.com/donaldtmcknight/microDecon) +microbiotaPair [An R Package for Simplified Microbiome Analysis Workflows on Intervention Study](https://github.com/rusher321/microbiotaPair) +MedTest [A Distance-Based Approach for Testing the Mediation Effect of the Human Microbiome](https://academic.oup.com/bioinformatics/article/34/11/1875/4810437) +MegaR [An Interactive R Package for Metagenomic Sample Classification and Disease Prediction using Microbiota and Machine Learning](https://github.com/BioHPC/MegaR) +MelonnPan [Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles](https://github.com/biobakery/melonnpan) +Metacoder [An R package for visualization and manipulation of community taxonomic diversity data](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005404) +metagenomeSeq [Differential abundance analysis for microbial marker-gene surveys](http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2658.html) +MetaLonDA [METAgenomic LONgitudinal Differential Abundance method](https://github.com/aametwally/MetaLonDA) +metamicrobiomeR [Analysis of Microbiome Relative Abundance Data using Zero Inflated Beta GAMLSS and Meta-Analysis Across Studies using Random Effects Model](https://github.com/cran/metamicrobiomeR) +metaSPARSim [An R tool for 16S rRNA-gene sequencing count data simulation](https://gitlab.com/sysbiobig/metasparsim) +microbiome R package [Tools for microbiome analysis in R](https://github.com/microbiome/microbiome) +MicrobiomeDDA [An Omnibus Test for Differential Distribution Analysis of Microbiome Sequencing Data](https://academic.oup.com/bioinformatics/article/34/4/643/4470360) +MicrobiomeHD [A standardized database of human gut microbiome studies in health and disease *Case-Control*](http://www.biorxiv.org/content/early/2017/05/08/134031) +microbiomeMarker [R package for microbiome biomarker discovery](https://github.com/yiluheihei/microbiomeMarker) +MicrobiomeR [MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows](https://microbiomer.vallenderlab.org/) +microbiomeutilities [Extending and supporting package based on microbiome and phyloseq R package](https://microsud.github.io/microbiomeutilities/) +MicrobiotaProcess [MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome](https://github.com/YuLab-SMU/MicrobiotaProcess) +miLineage [A General Framework for Association Analysis of Microbial Communities on a Taxonomic Tree](https://medschool.vanderbilt.edu/tang-lab/software/miLineage) +MINT [Multivariate INTegrative method](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1553-8) +mixDIABLO [Data Integration Analysis for Biomarker discovery using Latent variable approaches for ‘Omics studies](http://mixomics.org/mixdiablo/) +mixMC [Multivariate Statistical Framework to Gain Insight into Microbial Communities](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0160169) +MMinte [Methodology for the large-scale assessment of microbial metabolic interactions (MMinte) from 16S rDNA data](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1230-3) +MTA [Microbial trend analysis (MTA) for common dynamic trend, group comparison and classification in longitudinal microbiome study](https://github.com/chanw0/MTA) +MicrobiomeExplor [An R package for the analysis and visualization of microbial communities](https://doi.org/10.1093/bioinformatics/btaa838) +MicroBVS [Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03640-0) +MicroNiche [An R package for assessing microbial niche breadth and overlap from amplicon sequencing data](https://academic.oup.com/femsec/article-abstract/96/8/fiaa131/5863182?redirectedFrom=fulltext) +microViz [An R package for for analysis and visualization of microbiome sequencing data](https://david-barnett.github.io/microViz/) + +> N + +NMIT [Microbial Interdependence Association Test--a Non-parametric Microbial Interdependence Test](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5696116/#!po=75.0000) +NetCoMi [Network construction and comparison for microbiome data in R](https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa290/6017455) +NBZIMM [Negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03803-z) + +> O + +OMiSA [Optimal Microbiome-based Survival Analysis (OMiSA)](https://github.com/hk1785/OMiSA) + +> P + +pathostat [Statistical Microbiome Analysis on metagenomics results from sequencing data samples](https://bioconductor.org/packages/release/bioc/html/PathoStat.html) - [support deprecated](https://github.com/mani2012/PathoStat/issues/48) +phylofactor [Phylogenetic factorization of compositional data](https://peerj.com/articles/2969/) +phylogeo [Geographic analysis and visualization of microbiome data](https://www.ncbi.nlm.nih.gov/pubmed/25913208) +Phyloseq [Import, share, and analyze microbiome census data using R](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0061217) +Pldist [Pldist: Ecological Dissimilarities for Paired and Longitudinal Microbiome Association Analysis](https://academic.oup.com/bioinformatics/article-abstract/35/19/3567/5341424?redirectedFrom=fulltext) +powmic [Power assessment in microbiome case-control studies](https://github.com/lichen-lab/powmic) + +> Q + +qgraph [Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation](https://cran.r-project.org/web/packages/qgraph/qgraph.pdf) +qiime2R [Importing QIIME2 artifacts and associated data into R sessions](https://github.com/jbisanz/qiime2R) +qiimer [R tools compliment qiime](https://github.com/kylebittinger/qiimer) + +> R + +RAM [R for Amplicon-Sequencing-Based Microbial-Ecology](https://cran.r-project.org/web/packages/RAM/RAM.pdf) +RCM [A unified framework for unconstrained and constrained ordination of microbiome read count data](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205474) +RevEcoR [Reverse Ecology analysis in R](https://github.com/yiluheihei/RevEcoR) +Rhea [A pipeline with modular R scripts](https://peerj.com/articles/2836/) + +> S + +selbal [Balances: a New Perspective for Microbiome Analysis](https://msystems.asm.org/content/3/4/e00053-18) +ShinyPhyloseq [Web-tool with user interface for Phyloseq](http://joey711.github.io/shiny-phyloseq/) +SIAMCAT [Statistical Inference of Associations between Microbial Communities And host phenoTypes](https://bioconductor.org/packages/release/bioc/html/SIAMCAT.html) +SigTree [Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree](http://www.sciencedirect.com/science/article/pii/S2001037017300132) +SparseMCMM [Estimating and testing the microbial causal mediation effect with the high-dimensional and compositional microbiome data (SparseMCMM)](https://sites.google.com/site/huilinli09/software) +SPIEC-EASI [Sparse and Compositionally Robust Inference of Microbial Ecological Networks](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004226) +SplinectomeR [SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies](https://www.frontiersin.org/articles/10.3389/fmicb.2018.00785/full) +StructFDR [False Discovery Rate Control Incorporating Phylogenetic Tree Increases Detection Power in Microbiome-Wide Multiple Testing](https://academic.oup.com/bioinformatics/article/33/18/2873/3824757) +structSSI [Simultaneous and Selective Inference for Grouped or Hierarchically Structured Data](https://www.jstatsoft.org/article/view/v059i13) + +> T + +Tax4Fun [Predicting functional profiles from metagenomic 16S rRNA gene data](https://www.ncbi.nlm.nih.gov/pubmed/25957349) +taxize [Taxonomic Information from Around the Web](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3901538/) +TreeSummarizedExperiment [An extension class of SummarizedExperiment to allow hierarchical structure on the row or column dimension](https://github.com/fionarhuang/TreeSummarizedExperiment) +themetagenomics [Exploring Thematic Structure and Predicted Functionality of 16S rRNA Amplicon Data](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0219235) +tidyMicro [A pipeline for microbiome data analysis and visualization using the tidyverse in R](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-03967-2) + +> U + +> V + +vegan [R package for community ecologists](https://github.com/vegandevs/vegan) + +> X + +> Y + +yingtools2 [Tools and functions for working with clinical and microbiome data](https://github.com/ying14/yingtools2) + +> Z + +zeroSum [Reference Point Insensitive Molecular Data Analysis](https://academic.oup.com/bioinformatics/article/33/2/219/2928229) +ZIBBSeqDiscovery [A Zero-inflated Beta-binomial Model for Microbiome Data Analysis](https://onlinelibrary.wiley.com/doi/abs/10.1002/sta4.185)