Package: dar 1.1.0
Francesc Catala-Moll
dar: Differential Abundance Analysis by Consensus
Differential abundance testing in microbiome data challenges both parametric and non-parametric statistical methods, due to its sparsity, high variability and compositional nature. Microbiome-specific statistical methods often assume classical distribution models or take into account compositional specifics. These produce results that range within the specificity vs sensitivity space in such a way that type I and type II error that are difficult to ascertain in real microbiome data when a single method is used. Recently, a consensus approach based on multiple differential abundance (DA) methods was recently suggested in order to increase robustness. With dar, you can use dplyr-like pipeable sequences of DA methods and then apply different consensus strategies. In this way we can obtain more reliable results in a fast, consistent and reproducible way.
Authors:
dar_1.1.0.tar.gz
dar_1.1.0.zip(r-4.5)dar_1.1.0.zip(r-4.4)dar_1.1.0.zip(r-4.3)
dar_1.1.0.tgz(r-4.4-any)dar_1.1.0.tgz(r-4.3-any)
dar_1.1.0.tar.gz(r-4.5-noble)dar_1.1.0.tar.gz(r-4.4-noble)
dar_1.1.0.tgz(r-4.4-emscripten)dar_1.1.0.tgz(r-4.3-emscripten)
dar.pdf |dar.html✨
dar/json (API)
NEWS
| # Install 'dar' in R: |
| install.packages('dar', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/microbialgenomics-irsicaixaorg/dar/issues
- metaHIV_phy - Phyloseq object from metaHIV project
- test_prep_rec - PrepRecipe for metaHIV_phy data
- test_rec - Recipe for metaHIV_phy data
On BioConductor:dar-1.1.0(bioc 3.20)dar-1.0.0(bioc 3.19)
Last updated 2 months agofrom:b69c1d0831
Exports:abundance_pltadd_taxadd_varbakecontains_rarefactioncoolcorr_heatmapexclusion_pltexport_stepsfind_intersectionsget_phyget_taxget_varimport_stepsintersection_dfintersection_pltmutual_pltotu_tableoverlap_dfphy_qcpreprand_idread_datarecipesample_datastep_aldexstep_ancomstep_corncobstep_deseqstep_filter_by_abundancestep_filter_by_prevalencestep_filter_by_raritystep_filter_by_variancestep_filter_taxastep_lefsestep_maaslinstep_metagenomeseqstep_rarefactionstep_subset_taxastep_wilcoxsteps_idstax_tablezero_otu
Dependencies:abindade4apeaskpassassertthatbackportsbase64encbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularbiomformatBiostringsbitbit64bitopsblusterbootbslibcacachemCairocallrcaToolscheckmatecirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncrosstalkcurldata.tableDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsdendextenddiffobjdigestDirichletMultinomialdoParalleldplyrdqrngeggevaluatefansifarverfastmapFNNfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgclusgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggbeeswarmggplot2ggrastrggrepelGlobalOptionsgluegplotsgridExtragtablegtoolsheatmaplyhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrigraphIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelme4lpSolvemagrittrMASSMatrixMatrixGenericsmatrixStatsmediationmemoisemgcvmiamimeminqaMultiAssayExperimentmulttestmunsellmvtnormnlmenloptrnnetopensslopenxlsxpermutepheatmapphyloseqpillarpixmappkgconfigplotlyplyrpngprettyunitsprocessxprogresspromisespspurrrqapR.methodsS3R.ooR.utilsR6raggrappdirsrbiomRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppParallelRcppProgressreadrregistryrematch2reshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownrpartRSpectrarstudioapirsvdRtsneS4ArraysS4VectorssandwichsassScaledMatrixscalesscaterscuttleseriationshapeSingleCellExperimentsitmoslamsnowspSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttidytreetinytextreeioTreeSummarizedExperimentTSPtzdbUCSC.utilsUpSetRutf8uwotvctrsveganviporviridisviridisLitevroomwaldowebshotwithrxfunXVectoryamlyulab.utilszipzlibbioczoo
Converting Common Data Formats to Phyloseq and TreeSummarizedExperiment
Rendered fromdata_import.Rmdusingknitr::rmarkdownon Jun 30 2024.Last update: 2024-04-24
Started: 2022-08-19
Filtering and Subsetting
Rendered fromfiltering_subsetting.Rmdusingknitr::rmarkdownon Jun 30 2024.Last update: 2024-01-10
Started: 2023-11-29
Introduction to dar
Rendered fromdar.Rmdusingknitr::rmarkdownon Jun 30 2024.Last update: 2024-01-10
Started: 2022-08-19
Reproducibility in Microbiome Data Analysis
Rendered fromimport_export_recipes.Rmdusingknitr::rmarkdownon Jun 30 2024.Last update: 2023-11-29
Started: 2023-09-19
Workflow with real data
Rendered fromarticle.Rmdusingknitr::rmarkdownon Jun 30 2024.Last update: 2024-01-10
Started: 2023-01-31
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Abundance boxplot | abundance_plt abundance_plt,PrepRecipe-method abundance_plt,Recipe-method |
| Adds taxonomic level of interest in the Recipe. | add_tax add_tax,PrepRecipe-method add_tax,Recipe-method |
| Adds variable of interest to the Recipe | add_var add_var,PrepRecipe-method add_var,Recipe-method |
| Define consensus strategies from a Recipe | bake bake,PrepRecipe-method bake,Recipe-method |
| Checks if Recipe contains a rarefaction step | contains_rarefaction |
| Extract results from defined bake | cool cool,PrepRecipe-method cool,Recipe-method |
| Plot otuput of the 'overlap_df' function as a heatmap. | corr_heatmap corr_heatmap,PrepRecipe-method corr_heatmap,Recipe-method |
| Plot the number of shared DA OTUs between methods. | exclusion_plt exclusion_plt,PrepRecipe-method exclusion_plt,Recipe-method |
| Export step parameters as json. | export_steps |
| Finds common OTU between method results | find_intersections |
| Returns phyloseq from Recipe-class object | get_phy get_phy,Recipe-method |
| Returns tax_info from Recipe-class object | get_tax get_tax,Recipe-method |
| Returns var_info from Recipe-class object | get_var get_var,Recipe-method |
| Import steps from json file | import_steps |
| Returns data.frame with OTU intersection between methods | intersection_df intersection_df,PrepRecipe-method intersection_df,Recipe-method |
| Plot results using UpSet plot | intersection_plt intersection_plt,PrepRecipe-method intersection_plt,Recipe-method |
| Phyloseq object from metaHIV project | metaHIV_phy |
| Mutual finding plot | mutual_plt mutual_plt,PrepRecipe-method mutual_plt,Recipe-method |
| Extracts otu_table from phyloseq inside a Recipe | otu_table otu_table,Recipe-method |
| Overlap of significant OTUs between tested methods. | overlap_df overlap_df,PrepRecipe-method overlap_df,Recipe-method |
| Phyloseq Quality Control Metrics | phy_qc phy_qc,Recipe-method |
| Recipe-class object | phyloseq_or_null-class Recipe-class show,PrepRecipe-method tibble_or_NULL-class |
| Performs all the steps defined in a Recipe | prep prep,Recipe-method |
| PrepRecipe-class object | PrepRecipe-class |
| Make a random identification field for steps | rand_id |
| Create a Recipe for preprocessing data | Recipe recipe |
| Extracts sample_data from phyloseq inside a Recipe | sample_data sample_data,Recipe-method |
| ALDEx2 analysis | step_aldex step_aldex,PrepRecipe-method step_aldex,Recipe-method |
| ANCOM analysis | step_ancom step_ancom,PrepRecipe-method step_ancom,Recipe-method |
| corncob analysis | step_corncob step_corncob,PrepRecipe-method step_corncob,Recipe-method |
| DESeq2 analysis | step_deseq step_deseq,PrepRecipe-method step_deseq,Recipe-method |
| Filter taxa by abundance | step_filter_by_abundance step_filter_by_abundance,PrepRecipe-method step_filter_by_abundance,Recipe-method |
| Filter taxa by prevalence | step_filter_by_prevalence step_filter_by_prevalence,PrepRecipe-method step_filter_by_prevalence,Recipe-method |
| Filter taxa by rarity | step_filter_by_rarity step_filter_by_rarity,PrepRecipe-method step_filter_by_rarity,Recipe-method |
| Filter taxa by variance | step_filter_by_variance step_filter_by_variance,PrepRecipe-method step_filter_by_variance,Recipe-method |
| Filter taxa based on across-sample OTU abundance criteria | step_filter_taxa step_filter_taxa,Recipe-method |
| lefse analysis | step_lefse step_lefse,PrepRecipe-method step_lefse,Recipe-method |
| MaAsLin2 analysis | step_maaslin step_maaslin,PrepRecipe-method step_maaslin,Recipe-method |
| MetagenomeSeq analysis | step_metagenomeseq step_metagenomeseq,PrepRecipe-method step_metagenomeseq,Recipe-method |
| Resample an OTU table such that all samples have the same library size. | step_rarefaction step_rarefaction,PrepRecipe-method step_rarefaction,Recipe-method |
| Subset taxa by taxonomic level | step_subset_taxa step_subset_taxa,PrepRecipe-method step_subset_taxa,Recipe-method |
| Wilcox analysis | step_wilcox step_wilcox,PrepRecipe-method step_wilcox,Recipe-method |
| Get step_ids from recipe | steps_ids |
| Extracts tax_table from phyloseq inside a Recipe | tax_table tax_table,Recipe-method |
| PrepRecipe for metaHIV_phy data | test_prep_rec |
| Recipe for metaHIV_phy data | test_rec |
| Extract outs with all 0 values in at least on level of the variable | zero_otu zero_otu,phyloseq-method zero_otu,Recipe-method |
