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:
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')) |
Bug tracker:https://github.com/hannerlab/mdmapr/issues
Last updated 3 years agofrom:c86694736c. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 25 2024 |
R-4.5-win | OK | Oct 25 2024 |
R-4.5-linux | OK | Oct 25 2024 |
R-4.4-win | OK | Oct 25 2024 |
R-4.4-mac | OK | Oct 25 2024 |
R-4.3-win | OK | Oct 25 2024 |
R-4.3-mac | OK | Oct 25 2024 |
Exports:addThresholdCqdbInstancedbVariablesformatRawFluorescenceFilelaunchApp
Dependencies:abindaskpassbase64encberryFunctionsbslibcachemcellrangerclicolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdigestdplyrDTevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevalleafletleaflet.extrasleaflet.providerslifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlypngprettyunitsprogresspromisespurrrR6rappdirsrasterRColorBrewerRcppreactablereactRreadxlrematchrlangrmarkdownRMySQLsassscalesshinyshinydashboardshinyjsshinyWidgetssourcetoolsspstringistringrsysterratibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrwritexlxfunxtableyaml