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* Helpfile for RowSelection * Updated Helpfile for RowSelection * Updated Helpfile for DataSelection_Reset * Updated Helpfile for FileInput * Updated Helpfile for Upload via precompiled data. * Updated Helpfile for Metadata upload * Updated Helpfiles for Upload inspection and data download. * Helpfiles for preprocessing. Maybe Todo: add links? * Updated Helpfiles for EA * Updated Helpfiles for Heatmap * Updated Helpfiles for PCA * Updated Helpfiles for Sample Correlation * Updated Helpfiles for Sig Ana * Updated Helpfiles for Single Gene vis * Removed some unneccessary helpfiles * Update program/shinyApp/helpfiles/DataSelection_DataUploadFileInput.md Co-authored-by: Lea Seep <[email protected]> * Apply suggestions from code review Co-authored-by: Lea Seep <[email protected]> * Apply code suggestions. * Apply code suggestions. --------- Co-authored-by: Lea Seep <[email protected]>
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**DataInput** - Uploaded Omic Type: Lipidomics | ||
# ShinyOmics Report (18/12/2023) | ||
**AppVersion: 0.1.3 (2022-12-02)** | ||
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**DataInput** - The used data was precompiled. Filename: | ||
SHINY_LipidObsesityWTonly_precompiled 2022-06-27.rds | ||
## DataInput {.tabset .tabset-fade} | ||
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**DataInput** - The raw data dimensions are:502, 42 | ||
### Info | ||
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**DataInput** - Uploaded Omic Type: Transcriptomics | ||
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**DataInput** - Test Data set used | ||
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**DataInput** - All constant annotation entries for entities and samples are removed from the thin out the selection options! | ||
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**DataInput** - The raw data dimensions are:33469, 8 | ||
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### Publication Snippet | ||
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The Transcriptomics data was read into R (v. 4.2.1) (R Core Team (2022). _R: A Language and Environment for Statistical Computing_. R Foundationfor Statistical Computing, Vienna, Austria. <https://www.R-project.org/>.). The raw's data dimensions were: 33469, 8. All annotation that is constant over all samples is hidden within the Shiny-Application, as they do not provide any additional knowledge.This was done with the purrr package (v. 1.0.2)(Wickham H, Henry L (2023). _purrr: Functional Programming Tools_. R package version 1.0.2,<https://CRAN.R-project.org/package=purrr>.) | ||
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<br> | ||
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## Data Selection | ||
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**DataSelection** - The following selection was conducted: | ||
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**DataSelection** - Samples: | ||
DataSelection - based on: cell: all | ||
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**DataSelection** - Entities: | ||
DataSelection - based on: geneName: all | ||
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## Pre Processing | ||
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**PreProcessing** - As general remove all entities which are constant over all samples (automatically) | ||
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**PreProcessing** - Preprocessing procedure -standard (depending only on omics-type): Remove anything which row Count <= 10 | ||
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**PreProcessing** - Preprocessing procedure -specific (user-chosen): filterOnly | ||
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**PreProcessing** - The resulting dimensions are: 22008, 8 | ||
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