Package: SeroTrackR 1.1.1

"Dionne Argyropoulos, PhD"

SeroTrackR: Serology-Based Data Analysis and Visualization

Data wrangling and cleaning, quality control checks and implementation of machine learning classification algorithm.

Authors:Dionne Argyropoulos, PhD [aut, cre], Eamon Conway, PhD [aut], Caitlin Bourke, PhD [aut], Connie Li-Wai-Suen, PhD [aut], Shazia Ruybal-Pesántez, PhD [aut], Ivo Mueller, PhD [ctb], Rhea Longley, DPhil [ctb], Lauren Smith, PhD [aut]

SeroTrackR_1.1.1.tar.gz
SeroTrackR_1.1.1.zip(r-4.7-any)SeroTrackR_1.1.1.zip(r-4.6-any)SeroTrackR_1.1.1.zip(r-4.5-any)
SeroTrackR_1.1.1.tgz(r-4.6-any)SeroTrackR_1.1.1.tgz(r-4.5-any)
SeroTrackR_1.1.1.tar.gz(r-4.7-any)SeroTrackR_1.1.1.tar.gz(r-4.6-any)
SeroTrackR_1.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SeroTrackR/json (API)

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

Bug tracker:https://github.com/dionnecargy/serotrackr/issues

Pkgdown/docs site:https://dionnecargy.github.io

On CRAN:

Conda:

data-analysisserology

5.69 score 11 scripts 408 downloads 55 exports 145 dependencies

Last updated from:42c14239a3. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK180
source / vignettesOK337
linux-releaseOK182
macos-releaseOK218
macos-oldrelOK158
windows-develOK108
windows-releaseOK146
windows-oldrelOK159
wasm-releaseOK167

Exports:.check_platform.clean_bioplex.clean_luminex.convert_dilution_to_mfi.convert_mfi_to_dilution.convert_mfi_to_dilution_no_bounds.convert_mfi_to_dilution_no_lower_bound.extract_luminex_sections.fit_standard_curve.magpix_version_config.merge_mfitorau.post_process_bioplex.post_process_luminex.process_antigen_loglog.read_luminex_file.relabel_columns.setup_mfitorau_inputsclassifyResultsgetAntigenCountsgetCountsgetCountsQCgetGithubReleasegetPlateLayoutgetRepeatsgetSampleIDmakeCardMFItoRAUMFItoRAU_AdjMFItoRAU_LDHMFItoRAU_PkMFItoRAU_PlasmoplotBeadCountsplotBlanksplotBoxPlotClassificationplotCountsplotMFIplotModelplotModel_AdjplotRAUplotStdsplotStds_allplotStds_PkPfPvprocessCountsprocessPkPfPvreadPlateLayoutreadSeroDatarenderClassificationTablerenderDetailsListrenderQCReportrenderReportrenderTwoColsrunLDHPipelinerunPlasmoPipelinerunPvSeroPipelinerunQC

Dependencies:abindbackportsbase64encbootbroombslibcachemcarcarDatacellrangerclasscliclockcodetoolscolorspacecowplotcpp11crayondata.tableDerivdiagramdigestdoBydplyrdrcevaluatefarverfastmapfontawesomeforcatsforecastFormulafracdifffsfuturefuture.applygenericsggplot2globalsgluegowergtablegtoolshardhatherehighrhmshtmltoolsipredisobandjanitorjquerylibjsonlitekableExtraKernSmoothknitrlabelinglatticelavalifecyclelistenvlme4lmtestlubridatemagrittrMASSMatrixMatrixModelsmemoisemgcvmimeminqamodelenvmodelrmultcompmvtnormnlmenloptrnnetnumDerivopenxlsxparallellyparsnippbkrtestpillarpkgconfigplotrixprettyunitsprodlimprogressprogressrpurrrquantregR6rangerrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadxlrecipesreformulasrematchrlangrmarkdownrpartrprojrootrstudioapiS7sandwichsassscalesshapesnakecaseSparseMsparsevctrsSQUAREMstringistringrsurvivalsvglitesystemfontstextshapingTH.datatibbletidyrtidyselecttimechangetimeDatetinytextzdburcautf8vctrsviridisLitewithrworkflowsxfunxml2yamlzipzoo

Before You Begin
File Name Convention | Raw Data Files | Plate Layout File
Rendered fromsetup.Rmdusingknitr::rmarkdown

Last update: 2026-03-25
Started: 2025-12-02

FAQs
How do I install R packages other than SeroTrackR? | How do I organise my files? | How can I read in my data? | Is there capability to run this without internet? | I have multiple plate layout files. How can I input them? | I have multiple Luminex data types I'd like to analyse. How can I do this?
Rendered fromFAQs.Rmdusingknitr::rmarkdown

Last update: 2026-03-25
Started: 2025-12-02

Pk/Pv/Pf Serology Tutorial
Visualisation of the Pk/Pv/Pf Pipeline | 5-Point Standard Curve | Step 1: Load your data! | Step 2: Read your data and process MFI to RAU | Standard Curve Plot | Bead Counts QC Plot | Blanks QC Ploat | MFI to RAU Tables | 10-Point Standard Curve
Rendered fromPk_Pv_Pf_Serology_Tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-03-11
Started: 2025-12-02

PvSeroApp in R Tutorial
Data Analysis: runPvSeroPipeline() | Visualisation of the PvSeroApp Pipeline | Using Tutorial Dataset: Load the Data | Run Classification: Yes | Classification | Standard Curve Plot | Bead Counts QC Plot | Blanks QC Plot | Model Output Plot | Run Classification: No | MFI and RAU Data | QC Plots | Create a PDF Report
Rendered fromPvSeroApp_R_Tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-03-11
Started: 2025-07-23

PvLDH Tutorial
Data Analysis: LDH | Using Tutorial Dataset: Load the Data | Run Pipeline
Rendered fromPvLDH_Tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-03-11
Started: 2025-12-02

Readme and manuals

Help Manual

Help pageTopics
Check Platform.check_platform
Helper function to process bioplex data.clean_bioplex
Helper function to process luminex (Magpix/Intelliflex) data.clean_luminex
Convert known dilution to mfi from fitted standard curve.convert_dilution_to_mfi
Convert mfi to dilution using known standard curve fit..convert_mfi_to_dilution
Convert mfi to dilution using known standard curve fit and no bounds.convert_mfi_to_dilution_no_bounds
Convert mfi to dilution using known standard curve fit and no lower bound.convert_mfi_to_dilution_no_lower_bound
Helper function to process luminex sections.extract_luminex_sections
Fit a standard curve to known mfi and dilution values..fit_standard_curve
Helper function to identify Magpix version.magpix_version_config
Helper function to add Sample IDs to output..merge_mfitorau
Helper function to process bioplex sections.post_process_bioplex
Helper function to process luminex into master_list.post_process_luminex
Helper function to fit a 5-parameter logistic standard curve to dilutions.process_antigen_loglog
Helper function to read raw luminex files.read_luminex_file
Relabel column names to Standardised Naming Convention.relabel_columns
Helper function to set up MFI to RAU function.setup_mfitorau_inputs
Random Forest ClassificationclassifyResults
Example Serological Dataset: Bioplex Plate 1example_BioPlex_plate1_xlsx
Example Serological Dataset: Bioplex Plate 2example_BioPlex_plate2_xlsx
Example Serological Dataset: Bioplex Plate 3example_BioPlex_plate3_xlsx
Example Serological Dataset: Bioplex PvLDH Plate 1example_BioPlex_PvLDH_plate1_xlsx
Example Serological Dataset: MAGPIX Plate 1 Pk Analysis 10-Point Standard Curve A dataset containing raw MFI values and metadata from a sample plate run (MAGPIX).example_MAGPIX_pk_10std_plate1_csv
Example Serological Dataset: MAGPIX Plate 2 Pk Analysis 10-Point Standard Curveexample_MAGPIX_pk_10std_plate2_csv
Example Serological Dataset: MAGPIX Plate 1 Pk Analysis 5-Point Standard Curve A dataset containing raw MFI values and metadata from a sample plate run (MAGPIX).example_MAGPIX_pk_5std_plate1_csv
Example Serological Dataset: MAGPIX Plate 2 Pk Analysis 5-Point Standard Curveexample_MAGPIX_pk_5std_plate2_csv
Example Serological Dataset: MAGPIX Plate 1 A dataset containing raw MFI values and metadata from a sample plate run (MAGPIX).example_MAGPIX_plate1_csv
Example Serological Dataset: MAGPIX Plate 2example_MAGPIX_plate2_csv
Example Serological Dataset: MAGPIX Plate 3example_MAGPIX_plate3_csv
96 Well Plate Example Layoutexample_platelayout_1_xlsx
10-Point Standard Curve Example Plate Layoutexample_platelayout_pk_10std_xlsx
5-Point Standard Curve Example Plate Layoutexample_platelayout_pk_5std_xlsx
Get Count Data for each Antigen from the Raw Median Fluorescent IntensitygetAntigenCounts
Get Count Data from Raw Median Fluorescent IntensitygetCounts
Get All Counts DatagetCountsQC
Get GitHub VersiongetGithubRelease
Find and create a master plate layout filegetPlateLayout
Check Beads to RepeatgetRepeats
Get SampleID from Plate LayoutgetSampleID
Make Card in Fluent UImakeCard
Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversionMFItoRAU
Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion based on other standardMFItoRAU_Adj
Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion for LDHMFItoRAU_LDH
Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion for Pk proteinsMFItoRAU_Pk
Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion for Pk/Pf/Pv Master FunctionMFItoRAU_Plasmo
Plot Bead Counts per Plate per AntigenplotBeadCounts
Plot Raw Median Fluorescent Intensity Blanks DataplotBlanks
Plot ClassificationplotBoxPlotClassification
Plot Bead Count DataplotCounts
Median Fluorescent Intensity (MFI) Box PlotsplotMFI
Plot the Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) Results DataplotModel
Plot the Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) Results Data based on ETH standardplotModel_Adj
Relative Antibody Unit (RAU) Box PlotsplotRAU
Plot Raw Median Fluorescent Intensity of Standard Curve DataplotStds
Plot Raw Median Fluorescent Intensity of Standard Curve DataplotStds_all
Plot Raw Median Fluorescent Intensity of Pk/Pf/Pv Standard Curve DataplotStds_PkPfPv
Process Counts from Raw Serological Data fileprocessCounts
Processing Serological Data for Pk/Pf/Pv MFI to RAU conversionprocessPkPfPv
Read Plate Layout/sreadPlateLayout
Read Raw Serological DatareadSeroData
All Classification DatarenderClassificationTable
Create a Fluent UI TablerenderDetailsList
Generate QC PDF ReportrenderQCReport
Render Markdown reportrenderReport
Create two columns in Fluent UIrenderTwoCols
Run LDH Pipeline from Start to EndrunLDHPipeline
Run Pk/Pf/Pv Data Analysis Pipeline from Start to EndrunPlasmoPipeline
Run PvSero Pipeline from Start to EndrunPvSeroPipeline
Run Quality Control PipelinerunQC