Package: drugsens 0.1.0
drugsens: Automated Analysis of 'QuPath' Output Data and Metadata Extraction
A comprehensive toolkit for analyzing microscopy data output from 'QuPath' software. Provides functionality for automated data processing, metadata extraction, and statistical analysis of imaging results. The methodology implemented in this package is based on Labrosse et al. (2024) <doi:10.1016/j.xpro.2024.103274> "Protocol for quantifying drug sensitivity in 3D patient-derived ovarian cancer models", which describes the complete workflow for drug sensitivity analysis in patient-derived cancer models.
Authors:
drugsens_0.1.0.tar.gz
drugsens_0.1.0.zip(r-4.7-any)drugsens_0.1.0.zip(r-4.6-any)drugsens_0.1.0.zip(r-4.5-any)
drugsens_0.1.0.tgz(r-4.6-any)drugsens_0.1.0.tgz(r-4.5-any)
drugsens_0.1.0.tar.gz(r-4.7-any)drugsens_0.1.0.tar.gz(r-4.6-any)
drugsens_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
drugsens/json (API)
| # Install 'drugsens' in R: |
| install.packages('drugsens', repos = c('https://flalom.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/flalom/drugsens/issues
data-analysisimage-processingqupathworkflow
Last updated from:815d4cc23d. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 165 | ||
| source / vignettes | OK | 204 | ||
| linux-release | NOTE | 167 | ||
| macos-release | NOTE | 171 | ||
| macos-oldrel | NOTE | 250 | ||
| windows-devel | NOTE | 83 | ||
| windows-release | NOTE | 99 | ||
| windows-oldrel | NOTE | 97 | ||
| wasm-release | OK | 161 |
Exports:change_data_format_to_longerdata_bindinggenerate_qupath_scriptget_QC_plotsget_QC_plots_parsed_merged_datamake_count_dataframemake_run_configstring_parsing
Dependencies:abindbackportsbootbrewbriobroomcallrcarcarDataclicolorspacecommonmarkcorrplotcowplotcpp11crayonDerivdescdiffobjdoBydplyrevaluatefarverforecastFormulafracdifffsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrisobandjsonliteknitrlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmgcvminqamodelrnlmenloptrnnetnumDerivotelpbkrtestpillarpkgbuildpkgconfigpkgloadpolynompraiseprocessxpspurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackrdtoolsreformulasrlangroxygen2rprojrootrstatixS7scalesSparseMstringistringrsurvivaltestthattibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewaldowithrxfunxml2yamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Data format changer | change_data_format_to_longer |
| Merge all the dataframes coming out from the QuPath | data_binding |
| Generate the groovy script used for the analysis | generate_qupath_script |
| Plot some QC plots to define that everything ran correctly | get_QC_plots |
| Plot QC plots and calculate statistics for bound data | get_QC_plots_parsed_merged_data |
| Count the main marker expression | make_count_dataframe |
| Generates and use a config txt file | make_run_config |
| Parse image filenames to extract metadata | string_parsing |