Package: DspikeIn 1.3.0

Mitra Ghotbi

DspikeIn: Estimating Absolute Abundance from Microbial Spike-in Controls

Provides a reproducible and modular workflow for absolute microbial quantification using spike-in controls. Supports both single spike-in taxa and synthetic microbial communities with user-defined spike-in volumes and genome copy numbers. Compatible with 'phyloseq' and 'TreeSummarizedExperiment' (TSE) data structures. The package implements methods for spike-in validation, preprocessing, scaling factor estimation, absolute abundance conversion, bias correction, and normalization. Facilitates downstream statistical analyses with 'DESeq2', 'edgeR', and other Bioconductor-compatible methods. Visualization tools are provided via 'ggplot2', 'ggtree', and related packages. Includes detailed vignettes, case studies, and function-level documentation to guide users through experimental design, quantification, and interpretation.

Authors:Mitra Ghotbi [aut, cre], Marjan Ghotbi [ctb]

DspikeIn_1.3.0.tar.gz
DspikeIn_1.3.0.zip(r-4.7)DspikeIn_1.3.0.zip(r-4.6)DspikeIn_1.3.0.zip(r-4.5)
DspikeIn_1.3.0.tgz(r-4.6-any)DspikeIn_1.3.0.tgz(r-4.5-any)
DspikeIn_1.3.0.tar.gz(r-4.7-any)DspikeIn_1.3.0.tar.gz(r-4.6-any)
DspikeIn_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DspikeIn/json (API)
NEWS

# Install 'DspikeIn' in R:
install.packages('DspikeIn', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mghotbi/dspikein/issues

Datasets:
  • AcceptableRange - Acceptable Range Data
  • metadata_full - Metadata for Microbiome Samples
  • physeq - Example Phyloseq Object with Tree and Reference Sequences
  • physeq_16SOTU - Example Phyloseq Object for 16S OTUs
  • physeq_ITSOTU - Example Phyloseq Object for ITS OTUs
  • tse - Example TreeSummarizedExperiment (TSE) Object with Tree and Reference Sequences

On BioConductor:DspikeIn-1.3.0(bioc 3.24)DspikeIn-1.2.0(bioc 3.23)

microbiomepreprocessingqualitycontroldifferentialexpressionnormalizationsequencingvisualizationphylogeneticsexperimentaldesigndataimportsoftwareabsolute-abundancesamplicon-sequencinggene-copiesphylogenetic-treesqiime2quantifyingspike-instransformationwhole-cell

6.44 score 17 stars 36 scripts 219 downloads 61 exports 197 dependencies

Last updated from:7bf75c07b2. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE302
linux-devel-x86_64OK953
source / vignettesOK586
linux-release-x86_64OK882
macos-release-arm64OK550
macos-oldrel-arm64OK619
windows-develOK818
windows-releaseOK886
windows-oldrelOK809
wasm-releaseOK221

Exports:adjust_abundance_by_factoradjust_abundance_one_thirdadjusted_prevalencealluvial_plotcalculate_list_average_scaling_factorscalculate_spike_percentagecalculate_spike_percentage_listcalculate_spikeIn_factorscalculate_summary_stats_tablecolor_paletteconclusionconvert_categorical_to_factorsconvert_phyloseq_to_tseconvert_to_absolute_countsconvert_tse_to_phyloseqcreate_directorydegree_networkdetect_common_asvs_taxaextract_neighborsfilter_and_split_abundanceget_long_format_dataget_otu_tableget_phy_treeget_reference_seqget_sample_dataget_sample_sumsget_tax_tablegm_meanimbalance_calculate_list_average_scaling_factorslabelload_graphmlMG_shapesmy_custom_themenode_level_metricsnorm.DESeqnormalization_setperform_and_visualize_DAplot_core_microbiome_customplot_spikein_tree_diagnosticplotbar_abundancePre_processing_hashcodesPre_processing_speciesPre_processing_species_listproportion_adjquadrant_plotrandom_subsample_WithReductionFactorRandomForest_selectedrandomsubsample_Trimmed_evenDepthregression_plotrelativized_filtered_taxaremove_zero_negative_count_samplesridge_plot_itset_nfsimulate_network_robustnesssumm_ASV_OTUIDsumm_count_phyloseqsumm_phyloseq_sampleIDtaxa_barplottidy_phyloseq_tsevalidate_spikein_cladeweight_Network

Dependencies:abindade4apeaplotaskpassbackportsbase64encbayesmBHBiobaseBiocGenericsBiocParallelbiomformatBiostringsbootbroombslibcachemcarcarDatacliclustercodetoolscolorspacecompositionscorrplotcowplotcpp11crayondata.tableDBIDECIPHERDelayedArrayDEoptimRDerivDESeq2digestdoBydplyredgeRevaluatefarverfastmapfastmatchflextablefontawesomefontBitstreamVerafontLiberationfontquiverforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgdtoolsgenericsGenomicRangesggalluvialggforceggfunggiraphggnewscaleggplot2ggplotifyggpubrggraphggrepelggridgesggsciggsignifggstarggtreeggtreeExtragluegraphlayoutsgridExtragridGraphicsgtablehighrhtmltoolshtmlwidgetsigraphIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlatticelazyevallifecyclelimmalme4lmtestlocfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmicrobiomemimeminqamodelrmsamulttestnlmenloptrnnetnumDerivofficeropensslpatchworkpbkrtestpermutephangornphyloseqpillarpixmappkgconfigplyrpolyclippolynompurrrquadprogquantregR6raggrandomForestrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rlangrmarkdownrobustbaserstatixRtsneS4ArraysS4VectorsS7sassscalesSeqinfoSingleCellExperimentsnowspSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensorAtextshapingtibbletidygraphtidyrtidyselecttidytreetimeDatetinytextreeioTreeSummarizedExperimenttweenrurcautf8uuidvctrsveganviridisviridisLitewithrxfunxml2XVectoryamlyulab.utilszipzoo

DspikeIn with TSE

Mitra Ghotbi

Rendered fromDspikeIn-with-TSE.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2025-10-22
Started: 2025-06-18

Readme and manuals

Help Manual

Help pageTopics
Acceptable Range DataAcceptableRange
Adjust Abundance by a Custom Factoradjust_abundance_by_factor adjust_abundance_one_third
Adjust Prevalence in a Microbiome Objectadjusted_prevalence
Generate an Alluvial Plot for Microbiome Dataalluvial_plot
Calculate Sample-specific Average Scaling Factors for Multiple Spike-in Groupscalculate_list_average_scaling_factors
Calculate Spike Percentage for Specified Taxa in a Phyloseq or TSE Objectcalculate_spike_percentage
Calculate Spike-in Percentage for Specified Taxacalculate_spike_percentage_list
Calculate Scaling Factors for Spiked Species in Phyloseq or TSE Objectcalculate_spikeIn_factors
Calculate Summary Statistics Tablecalculate_summary_stats_table
Original, Extended, and Nature-Inspired Color Palette Sequencecolor_palette
Compute Summary Statistics for Spiked Speciesconclusion
Convert Categorical Columns to Factors in Sample Dataconvert_categorical_to_factors
Convert a 'phyloseq' Object to a 'TreeSummarizedExperiment'convert_phyloseq_to_tse
Convert Relative ASV/OTU Counts to Absolute Countsconvert_to_absolute_counts
Convert a 'TreeSummarizedExperiment' to a 'phyloseq' Objectconvert_tse_to_phyloseq
Create a Directory and Optionally Set as Working Directorycreate_directory
Create a List from a Phyloseq or TSE Objectcreate_list
Analyze and Visualize a Microbial Networkdegree_network
Detect Common ASVs and Taxa from Multiple Phyloseq or TSE Objectsdetect_common_asvs_taxa
Extract First and Second Neighbors of a Target Nodeextract_neighbors
Filter and Split Abundance Data by Thresholdfilter_and_split_abundance
Convert a Phyloseq or TSE Object into a Long-Format Data Frameget_long_format_data
Extract OTU Tax Metadata from Objectget_otu_table
Extract Phylogenetic Treeget_phy_tree
Extract Reference Sequencesget_reference_seq
Extract Sample Dataget_sample_data
Extract Sample Sums from Objectget_sample_sums
Extract Taxonomy Tableget_tax_table
Calculate Geometric Meangm_mean
Calculate Per-Sample Scaling Factors for Multiple Spike-in Groupsimbalance_calculate_list_average_scaling_factors
Label Taxonomic Ranks by Hashcodelabel
Load GraphML Without 'id' Conflictsload_graphml
Metadata for Microbiome Samplesmetadata_full
Predefined Shape Vector for Plot StylingMG_shapes
Custom ggplot2 Theme with Consistent Aestheticsmy_custom_theme
Compute and Visualize Node-Level Network Metricsnode_level_metrics
CLR Normalization (Centered Log-Ratio Transformation)norm.clr
CSS Normalization (Cumulative Sum Scaling)norm.css
DESeq Normalization with Pseudocount and Integer Conversionnorm.DESeq
Median Normalizationnorm.med
Poisson Normalization and Differential Abundance Functionnorm.Poisson
Quantile Normalization (QN) for phyloseq objectnorm.QN
Rarefyingnorm.rar
RLE Normalization (Relative Log Expression)norm.rle
TC Normalization (Total Count Scaling)norm.TC
TMM Normalization (Trimmed Mean of M component)norm.TMM
TSS Normalization (Total Sum Scaling)norm.tss
UQ Normalization (Upper Quartile)norm.UQ
Apply the Selected Normalization Method to the Phyloseq and TSE Objectsnormalization_set
Perform and Visualize Differential Abundance Analysis with edgeR or DESeq2perform_and_visualize_DA
Example Phyloseq Object with Tree and Reference Sequencesphyseq
Example Phyloseq Object for 16S OTUsphyseq_16SOTU
Example Phyloseq Object for ITS OTUsphyseq_ITSOTU
Plot Core Microbiome Prevalence Heatmap (Phyloseq & TSE Compatible)plot_core_microbiome_custom
Spike-in Tree Diagnostic Plotplot_spikein_tree_diagnostic
Taxa Bar Plot Without Aggregation (Relative or Absolute Abundance)plotbar_abundance
Pre-process phyloseq or TSE object based on hashcodesPre_processing_hashcodes
Pre-process taxa in a phyloseq or TSE object by merging ASVs/OTUsPre_processing_species
Preprocess and Merge Spike-in Species in a Phyloseq or TSE ObjectPre_processing_species_list
Proportionally Adjust Abundanceproportion_adj
Generate Custom Quadrant Plots for Node Metricsquadrant_plot
Random Subsampling with Reduction Factorrandom_subsample_WithReductionFactor
Select Important ASVs/OTUs Using Random ForestRandomForest_selected
Subsampling to an Equal Sequencing Depthrandomsubsample_Trimmed_evenDepth
Create a Regression Plot with Faceting by Rangeregression_plot
Filter Taxa from a Phyloseq or TSE Object Based on Custom Thresholdsrelativized_filtered_taxa
Remove Samples with Zero, Negative Counts, or NA Values and Add Pseudocountremove_zero_negative_count_samples
Generate Ridge Plots for Taxonomic Abundance Distributionridge_plot_it
Set Normalization Factors in the Sample Data of the Phyloseq Objectset_nf
Simulate Network Robustness under Node Removalsimulate_network_robustness
Summarize ASV Data Based on ASV_IDsumm_ASV_OTUID
Summary Statistics of a Phyloseq or TSE Objectsumm_count_phyloseq
Generate Summary Statistics for Each Samplesumm_phyloseq_sampleID
Generate a Taxa Barplot with Relative or Absolute Abundancetaxa_barplot
Tidy a Phyloseq or TreeSummarizedExperiment Objecttidy_phyloseq_tse
Example TreeSummarizedExperiment (TSE) Object with Tree and Reference Sequencestse
Validate Spike-In Clade Consistency with NJ Tree and Bootstrapvalidate_spikein_clade
Analyze and Visualize a Microbial Networkweight_Network