Aim of this package | Important to Know Before You Start | Workflow | Step 1: Prepare your Data | Step 2: Read your Data with read_folder() function | Step3: Check your data with qc_data() function | Step 4 (Optional): Visualize the Final Timepoint: plot_latest_timepoint() | Step 5: Annotate Chemicals to PlateType and Well with annotate_chemical() | Custom annotation files | Step 6: Quality control of OD curves | Step 7: Summarize curves to Area under Curve (AUC) | Step 9: Check Control Well Variability | Step 10: Compare AUCs Per Plate | Step 11: Normalize AUC to AUC ratios and visualize | Step 12: Annotation of metadata | Step 13: Visualiation of AUC Ratios by group
Package: MetPhenoR 1.3
MetPhenoR: A Transparent Analysis Pipeline for Mammalian Metabolic Phenotype Microarray Data
Provides a transparent, end-to-end workflow for analyzing high-throughput phenotype microarray data in mammalian cell cultures. It begins with automated reading and noise correction, followed by comprehensive quality control via visual diagnostics, i.e. detecting missing wells, anomalous curve shapes and variance. Area under Curve is computed as a summary metric. Biological annotations (custom or in-built for PM-M01,PM-M02, PM-M11 - PM-M14) enable group-level comparisons.
Authors:
MetPhenoR_1.3.tar.gz
MetPhenoR_1.3.zip(r-4.7-any)MetPhenoR_1.3.zip(r-4.6-any)MetPhenoR_1.3.zip(r-4.5-any)
MetPhenoR_1.3.tgz(r-4.6-any)MetPhenoR_1.3.tgz(r-4.5-any)
MetPhenoR_1.3.tar.gz(r-4.7-any)MetPhenoR_1.3.tar.gz(r-4.6-any)
MetPhenoR_1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MetPhenoR/json (API)
| # Install 'MetPhenoR' in R: |
| install.packages('MetPhenoR', repos = c('https://katjadanielzik.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/katjadanielzik/metphenor/issues
Datasets:
- PlateInfo - An example '..._PlateInfo.csv" file
- PM_M01_M02 - Annotations for metabolic plates PM-M01 and PM-M02
- PM_M11_M14 - Annotations for anti-cancer drug plates PM-M11 to PM-M14
- processed_data - Example data set as result of read_folder.R with sample_column = "Sample" and variables = c
- RawRead - Example Raw Read from Odin Biolog
high-throughputmammalianmetabolismmicroarrayodinphenotyping
Last updated from:215c2e3479. Checks:2 NOTE, 7 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 184 | ||
| source / vignettes | OK | 214 | ||
| linux-release | OK | 172 | ||
| macos-release | OK | 204 | ||
| macos-oldrel | OK | 204 | ||
| windows-devel | NOTE | 223 | ||
| windows-release | OK | 292 | ||
| windows-oldrel | OK | 242 | ||
| wasm-release | OK | 116 |
Exports:annotate_chemicalannotate_metadataclassify_growth_curve_typescompute_auc_cicompute_auc_ratiofilter_dataplot_aucplot_auc_ratio_by_groupplot_auc_ratio_heatmapplot_auc_ratio_violinplot_controls_tween_all_plateplot_controls_tween_per_plateplot_growth_curveplot_latest_timepointqc_dataread_folder
Dependencies:base64encbitbit64clicliprcpp11crayondplyrfarvergenericsggforceggplot2gluegtablehmsisobandjsonlitelabelinglifecyclemagrittrMASSpatchworkpillarpkgconfigpolyclipprettyunitsprogresspurrrR6RColorBrewerreadrrlangS7scalesstringistringrsystemfontstibbletidyrtidyselecttweenrtzdbutf8vctrsviridisLitevroomwithr
