Package: MDMAPR 0.2.3

MDMAPR: Molecular Detection Mapping and Analysis Platform

Runs a Shiny web application that merges raw 'qPCR' fluorescence data with related metadata to visualize species presence/absence detection patterns and assess data quality. The application calculates threshold values from raw fluorescence data using a method based on the second derivative method, Luu-The et al (2005) <doi:10.2144/05382RR05>, and utilizes the ‘chipPCR’ package by Rödiger, Burdukiewicz, & Schierack (2015) <doi:10.1093/bioinformatics/btv205> to calculate Cq values. The application has the ability to connect to a custom developed MySQL database to populate the applications interface. The application allows users to interact with visualizations such as a dynamic map, amplification curves and standard curves, that allow for zooming and/or filtering. It also enables the generation of customized exportable reports based on filtered mapping data.

Authors:Alka Benawra <alkabenawra@rogers.com>

MDMAPR_0.2.3.tar.gz
MDMAPR_0.2.3.zip(r-4.5)MDMAPR_0.2.3.zip(r-4.4)MDMAPR_0.2.3.zip(r-4.3)
MDMAPR_0.2.3.tgz(r-4.5-any)MDMAPR_0.2.3.tgz(r-4.4-any)MDMAPR_0.2.3.tgz(r-4.3-any)
MDMAPR_0.2.3.tar.gz(r-4.5-noble)MDMAPR_0.2.3.tar.gz(r-4.4-noble)
MDMAPR_0.2.3.tgz(r-4.4-emscripten)MDMAPR_0.2.3.tgz(r-4.3-emscripten)
MDMAPR.pdf |MDMAPR.html✨
MDMAPR/json (API)

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

Bug tracker:https://github.com/hannerlab/mdmapr/issues

On CRAN:

Conda:

1.70 score 1 scripts 354 downloads 1 mentions 5 exports 100 dependencies

Last updated 4 years agofrom:c86694736c. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 24 2025
R-4.5-winOKMar 24 2025
R-4.5-macOKMar 24 2025
R-4.5-linuxOKMar 24 2025
R-4.4-winOKMar 24 2025
R-4.4-macOKMar 24 2025
R-4.4-linuxOKMar 24 2025
R-4.3-winOKMar 24 2025
R-4.3-macOKMar 24 2025

Exports:addThresholdCqdbInstancedbVariablesformatRawFluorescenceFilelaunchApp

Dependencies:abindaskpassbase64encberryFunctionsbslibcachemcellrangerclicolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdigestdplyrDTevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleafletleaflet.extrasleaflet.providerslifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlypngprettyunitsprogresspromisespurrrR6rappdirsrasterRColorBrewerRcppreactablereactRreadxlrematchrlangrmarkdownRMySQLsassscalesshinyshinydashboardshinyjsshinyWidgetssourcetoolsspstringistringrsysterratibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrwritexlxfunxtableyaml

Citation

To cite package ‘MDMAPR’ in publications use:

Benawra A (2021). MDMAPR: Molecular Detection Mapping and Analysis Platform. R package version 0.2.3, https://CRAN.R-project.org/package=MDMAPR.

ATTENTION: This citation information has been auto-generated from the package DESCRIPTION file and may need manual editing, see ‘help("citation")’.

Corresponding BibTeX entry: 

  @Manual{,
    title = {MDMAPR: Molecular Detection Mapping and Analysis
      Platform},
    author = {Alka Benawra},
    year = {2021},
    note = {R package version 0.2.3},
    url = {https://CRAN.R-project.org/package=MDMAPR},
  }