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 <[email protected]>

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-4.4-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'))

Peer review:

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

On CRAN:

1.70 score 1 scripts 361 downloads 1 mentions 5 exports 100 dependencies

Last updated 3 years agofrom:c86694736c. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-winOKOct 25 2024
R-4.5-linuxOKOct 25 2024
R-4.4-winOKOct 25 2024
R-4.4-macOKOct 25 2024
R-4.3-winOKOct 25 2024
R-4.3-macOKOct 25 2024

Exports:addThresholdCqdbInstancedbVariablesformatRawFluorescenceFilelaunchApp

Dependencies:abindaskpassbase64encberryFunctionsbslibcachemcellrangerclicolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdigestdplyrDTevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleafletleaflet.extrasleaflet.providerslifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlypngprettyunitsprogresspromisespurrrR6rappdirsrasterRColorBrewerRcppreactablereactRreadxlrematchrlangrmarkdownRMySQLsassscalesshinyshinydashboardshinyjsshinyWidgetssourcetoolsspstringistringrsysterratibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrwritexlxfunxtableyaml