Add tool list

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

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.

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)