Package: normfluodbf 2.0.0
normfluodbf: Cleans and Normalizes FLUOstar DBF and DAT Files from 'Liposome' Flux Assays
Cleans and Normalizes FLUOstar DBF and DAT Files obtained from liposome flux assays. Users should verify extended usage of the package on files from other assay types.
Authors:
normfluodbf_2.0.0.tar.gz
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normfluodbf_2.0.0.tgz(r-4.4-any)normfluodbf_2.0.0.tgz(r-4.3-any)
normfluodbf_2.0.0.tar.gz(r-4.5-noble)normfluodbf_2.0.0.tar.gz(r-4.4-noble)
normfluodbf_2.0.0.tgz(r-4.4-emscripten)normfluodbf_2.0.0.tgz(r-4.3-emscripten)
normfluodbf.pdf |normfluodbf.html✨
normfluodbf/json (API)
NEWS
| # Install 'normfluodbf' in R: |
| install.packages('normfluodbf', repos = c('https://alphaprime7.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/alphaprime7/normfluodbf/issues
- dat_1 - Dat_1.
- dat_2 - Dat_2.
- dat_3 - Dat_3.
- dat_4 - Dat_4.
- dat_5 - Dat_5.
- dat_6 - Dat_6.
- dat_7 - Dat_7.
- liposomes_214 - Liposomes_214.
- liposomes_215 - Liposomes_215.
- liposomes_216 - Liposomes_216.
- liposomes_218 - Liposomes_218.
- liposomes_221 - Liposomes_221.
- liposomes_227 - Liposomes_227.
Last updated 17 days agofrom:552e6b0309. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 06 2024 |
| R-4.5-win | OK | Nov 06 2024 |
| R-4.5-linux | OK | Nov 06 2024 |
| R-4.4-win | OK | Nov 06 2024 |
| R-4.4-mac | OK | Nov 06 2024 |
| R-4.3-win | OK | Nov 06 2024 |
| R-4.3-mac | OK | Nov 06 2024 |
Exports:.next_step.step_nameactual_cols_usedactual_cyclesactual_rows_usedadd_package_namespaceanalyze_readyaverage_fluorescence_by_row_cyclecapitalizecheck_broken_packagescheck_cols_classcheck_dirtcheck_package_usagecheck_stepchild_plate_typeclean_commasclean_even_datclean_odddat_optimuscomma_cleanercomment_out_linesdat_col_names_horizontaldat_col_names_optimusdat_col_names_primedat_col_names_rigiddecimal_scalingdecimal_scaling_dfdefine_paramsdefine_statusdefine_stepsdetect_outliers_cndetect_outliers_time_cndirtydirty<-empty_platefind_known_liposome_dat_filefind_known_liposome_dbf_filefind_random_portfix_threshold_outputfluor_threshold_checkfluor_threshold_check_naformat_plate_datageneric_identifierget_common_dat_namesget_dat_common_nameget_dat_file_nameget_dbf_file_nameget_single_wellget_status_valueget_step_key_by_indexget_tnpget_wells_btwnget_wells_usedhas_stepinit_plateis_diris_fileis_normalizedis_plate_dirtyis_rangeis_threshold_violatedlaunchlist_datslist_dbfsload_plate_dataload_plate_data<-load_plate_metaload_plate_meta<-load_rds_platelog_transformationmin_max_normmin_max_norm_dfmin_max_norm_percentmin_max_norm_percent_dfmodify_plate_datamove_filemultiplotnamename<-new_platenext_stepnorm_appliernorm_tidy_dbfnorm_znorm_z_dfnormalizenormalize_by_wellnormalize_dataframenormfluodatnormfluodatfullnormfluodatlitenormfluodbfnormfluodbf_datanormfluordatnormfluordbfopen_testfileparamsparams<-parent_plate_typepkg_globals_cacheplate_dataplate_data_summaryplate_metaplate_typesplate_types_tblplate_types_vectorplot_gridquietrange_list_to_vecrange_to_endpointsremove_leading_zeroremove_outliersreplace_word_in_fileresample_datresample_dat_altresample_dat_scaleresample_dat_scale_altresample_dat_scale_alt_bf_naresample_dat_scale_alt_bfvresample_dat_scale_alt_naresample_dat_scale_naretainerresample_dat_scale_optimusresample_dat_scale_optimus_backendresample_dat_scale_optimus_naresample_dat_vectresample_vect_scalereset_plateroundfluorrun_demorun_demo_bgrun_demo_in_backgroundrun_demo_scriptrun_stepssample_data_dirsample_data_filesave_platesave_plotsave_rds_platesearch_pkgset_assiette_typeset_default_paramsset_default_statusset_default_stepsset_plate_typeset_plate_versionsetup_plateshiny_random_portstatusstatus<-stepstep_beginstep_endstep_namestepssteps_completesteps<-subsetsubset_for_layoutsubset_unplated_datatest_boilerplatetime_ittypeunique_identifierupdate_status_listupdate_steps_listupload_datause_initialized_plateuse_setup_platevar_strviewerpane_background_normfluodbfx_var_onex_var_one_labelx_var_one_label<-x_var_one<-x_var_twox_var_two_labelx_var_two_label<-x_var_two<-y_vary_var<-
Dependencies:askpassassertthatbadgerbase64encBiocManagerbriobslibcachemcallrclicliprcolorspacecommonmarkcpp11crayoncredentialscrosstalkcurldata.tabledescdiffobjdigestdlstatsdplyremojifontevaluatefansifarverfastmapfontawesomeforcatsforeignfsgenericsgertggfunggimageggplot2ggplotifyghgitcredsgluegridExtragridGraphicsgtablehexbinhexStickerhighrhtmltoolshtmlwidgetshttpuvhttrhttr2iniisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagickmagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpbdZMQpillarpkgbuildpkgconfigpkgloadpkgsearchplotlypraiseprocessxpromisesprotopspurrrR6rappdirsRColorBrewerRcpprlangrmarkdownrprojrootrstudioapirvchecksassscalesshinyshowtextshowtextdbsourcetoolsstringistringrsyssysfontstestthattibbletidyrtidyselecttinytexusethisutf8vctrsviridisLitewaldowesandersonwhiskerwithrxfunxtableyamlyulab.utilszip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The %there% operator | %there% |
| Add Package Namespace | add_package_namespace |
| Analyze | analyze analyze_ready analyze_ready.1536well_plate_t1 analyze_ready.1536well_plate_t2 analyze_ready.384well_plate analyze_ready.96well_plate analyze_ready.default |
| Capitalize | average_fluorescence_by_row_cycle |
| Capitalize | capitalize |
| Check Broken Packages | check_broken_packages |
| Check Dirt | check_dirt |
| Check package or function Usage | check_package_usage |
| Child Type | childtype child_plate_type child_plate_type.default child_plate_type.normfluodbf_plate |
| DAT file data frame cleaner. | clean_commas |
| DAT file wrangler. | clean_even_dat clean_odddat_optimus |
| Comma Cleaner function. | comma_cleaner |
| Comment Out | comment_out_lines |
| dat_1. | dat_1 |
| dat_2. | dat_2 |
| dat_3. | dat_3 |
| dat_4. | dat_4 |
| dat_5. | dat_5 |
| dat_6. | dat_6 |
| dat_7. | dat_7 |
| Attribute(s) naming function. | dat_col_names_horizontal |
| Attribute(s) naming function. | dat_col_names_optimus |
| Attribute(s) naming function. | dat_col_names_prime |
| Attribute(s) naming function. | dat_col_names_rigid |
| Define Plate Parameters | defineparams define_params define_params.1536well_plate_t1 define_params.1536well_plate_t2 define_params.384well_plate define_params.96well_plate define_params.default set_default_params |
| Define Plate Status | definestatus define_status define_status.1536well_plate_t1 define_status.1536well_plate_t2 define_status.384well_plate define_status.96well_plate define_status.default get_status_value set_default_status update_status_list |
| Define Plate Steps | definesteps define_steps define_steps.1536well_plate_t1 define_steps.1536well_plate_t2 define_steps.384well_plate define_steps.96well_plate define_steps.default define_steps.normfluodbf_plate set_default_steps update_steps_list |
| Detect Outliers | detectoutliers detect_outliers_cn detect_outliers_time_cn |
| Directory Utils | dirutils find_known_liposome_dat_file find_known_liposome_dbf_file is_dir is_file list_dats list_dbfs |
| Random Port Normfluodbf Style | find_random_port |
| Format Plate Data | formatplatedata format_plate_data format_plate_data.1536well_plate_t1 format_plate_data.1536well_plate_t2 format_plate_data.384well_plate format_plate_data.96well_plate format_plate_data.default |
| Wells Used | get_wells_used |
| Get File Name(s) | getfilename get_common_dat_names get_dat_common_name get_dat_file_name get_dbf_file_name |
| Globals Cache | globalcache |
| Is Normalized | isnormalized is_normalized |
| Run the shiny App checking dependencies in R code ... WARNING In addition to the functions provided in this package, the 'normfluodbf' package also provides an interactive tool that can be used to analyze liposome flux assay data more easily. The tool will be launched in a web browser. | launch |
| Cleans and Normalizes DBF files obtained from experiments using the FLUOstar Omega microplate reader (from BMG LABTECH). | liposome_fluor_dbfs normfluodbf normfluordbf norm_tidy_dbf |
| liposomes_214. | liposomes_214 |
| liposomes_215. | liposomes_215 |
| liposomes_216. | liposomes_216 |
| liposomes_218. | liposomes_218 |
| liposomes_221. | liposomes_221 |
| liposomes_227. | liposomes_227 |
| Load Plate Data | loadplatedata load_plate_data load_plate_data<- |
| Load Plate Meta | loadplatemeta load_plate_meta load_plate_meta<- |
| Modify Plate Data | modifyplatedata modify_plate_data modify_plate_data.1536well_plate_t1 modify_plate_data.1536well_plate_t2 modify_plate_data.384well_plate modify_plate_data.96well_plate modify_plate_data.default |
| Move File | move_file |
| Multiplot | multiplot |
| Normalize | normalize normalize.1536well_plate_t1 normalize.1536well_plate_t2 normalize.384well_plate normalize.96well_plate normalize.default normalize_dataframe |
| Normalize by Well | normalizebywell normalize_by_well normalize_by_well.1536well_plate_t1 normalize_by_well.1536well_plate_t2 normalize_by_well.384well_plate normalize_by_well.96well_plate normalize_by_well.default |
| Normalizing Agents | decimal_scaling decimal_scaling_df log_transformation min_max_norm min_max_norm_df min_max_norm_percent min_max_norm_percent_df normalizingagents norm_z norm_z_df roundfluor |
| Plot Plate - Favorite is Fluostar style | normfluodbfplots plot.1536well_plate_t1 plot.1536well_plate_t2 plot.384well_plate plot.96well_plate |
| Cleans and normalizes DAT files obtained from experiments using the FLUOstar Omega microplate reader (from BMG LABTECH). | normfluodat normfluodatfull normfluodatlite normfluordat |
| Parent Type | parenttype parent_plate_type parent_plate_type.1536well_plate_t1 parent_plate_type.1536well_plate_t2 parent_plate_type.384well_plate parent_plate_type.96well_plate parent_plate_type.default parent_plate_type.normfluodbf_plate |
| Plate | empty_plate init_plate new_plate plate reset_plate setup_plate use_initialized_plate use_setup_plate |
| Plate Data Summary | plate_data_summary |
| Plate Types Tibble | plate_types plate_types_tbl plate_types_vector |
| Plate Data | platedata plate_data |
| Plate Meta | platemeta plate_meta plate_meta.1536well_plate_t1 plate_meta.1536well_plate_t2 plate_meta.384well_plate plate_meta.96well_plate plate_meta.default |
| Plate Name | name name<- platename |
| print.1536well_plate_t1 print.1536well_plate_t2 print.384well_plate print.96well_plate printer | |
| Quiet | quiet |
| Format Well Names | remove_leading_zero |
| Outliers | removeoutliers remove_outliers remove_outliers.1536well_plate_t1 remove_outliers.1536well_plate_t2 remove_outliers.384well_plate remove_outliers.96well_plate remove_outliers.default |
| Replace Word | replace_word_in_file |
| A function to create an attribute or column for each sample loaded into the microplate wells. | resample_dat_scale resample_dat_scale_alt resample_dat_scale_alt_bfv resample_dat_scale_alt_bf_na resample_dat_scale_alt_na resample_dat_scale_naretainer resample_dat_scale_optimus resample_dat_scale_optimus_backend resample_dat_scale_optimus_na resample_vect_scale |
| A function to create an attribute or column for each sample loaded into the microplate wells. | resample_dat resample_dat_alt resample_dat_vect |
| Run the shiny App In addition to the functions provided in this package, the 'normfluodbf' package also provides an interactive tool that can be used to analyze liposome flux assay data more easily. The tool will be launched in a web browser. | run_demo |
| Run Demo Background | run_demo_bg |
| Run Demo in Background | run_demo_in_background |
| Run Demo Script | run_demo_script |
| Get Development Data | sampledata sample_data_dir sample_data_file |
| Save and Load Plate | load_rds_plate saveloadutils save_plate save_rds_plate var_str |
| Set The Plate Types | set_assiette_type |
| Set The Child Plate Type | set_plate_type |
| Plate Version | set_plate_version |
| Set Plate Steps | setsteps steps steps<- |
| Random Port gptstudio style | shiny_random_port |
| Status | dirty dirty<- is_plate_dirty status status<- |
| Steps Pipeline | .next_step next_step run_steps stepspipeline |
| Steps Utils | .step_name check_step get_step_key_by_index has_step step stepsutils steps_complete step_begin step_end step_name |
| Test Boilerplate | open_testfile test_boilerplate |
| Plate Type | type |
| Upload Plate Data | uploadplatedata upload_data upload_data.1536well_plate_t1 upload_data.1536well_plate_t2 upload_data.384well_plate upload_data.96well_plate upload_data.default |
| View App in Viewer Pane | viewerpane_background_normfluodbf |
| Validate URL | wait_for_bg_shinyapp |
| Plot Coordinates | xycoordinates x_var_one x_var_one<- x_var_one_label x_var_one_label<- x_var_two x_var_two<- x_var_two_label x_var_two_label<- y_var y_var<- |
