Search results for "Reproducible research"
showing 4 items of 4 documents
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
2019
AbstractBackgroundPrincipal component analysis (PCA) is frequently useentirely written ind in genomics applications for quality assessment and exploratory analysis in high-dimensional data, such as RNA sequencing (RNA-seq) gene expression assays. Despite the availability of many software packages developed for this purpose, an interactive and comprehensive interface for performing these operations is lacking.ResultsWe developed the pcaExplorer software package to enhance commonly performed analysis steps with an interactive and user-friendly application, which provides state saving as well as the automated creation of reproducible reports. pcaExplorer is implemented in R using the Shiny fra…
sar: Automatic generation of statistical reports using Stata and Microsoft Word for Windows
2013
The output provided by most Stata commands is plain text not suitable to be presented or published. After the numerical and graphical outputs are obtained, the user has to copy them into a word processor to complete the editing process. Some Stata commands help you to obtain well-formatted output, especially tabulated results in LATEX or other formats, but they are not a complete solution nor are they friendly tools. Stata automatic report (Sar) is an easy-to-use macro for Microsoft Word for Windows that allows a powerful integration between Stata and Word. With Sar, the user can retrieve numerical results and graphs from Stata and automatically insert them into a well-formatted Word docum…
ideal: an R/Bioconductor package for interactive differential expression analysis
2020
AbstractBackgroundRNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but still provide flexibility and transparency in the adopted methods. Despite the availability of many packages focused on detecting differential expression, a method to streamline this type of bioinformatics analysis in a comprehensive, accessible, and reproducible way is lacking.ResultsWe developed the ideal software package, which serves as a web application for interactive and reproducible RNA-seq analysis, while producing a wealth of visualizations to facilitate data interpr…
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
2021
AbstractBackgroundThe interpretation of results from transcriptome profiling experiments via RNA sequencing (RNA-seq) can be a complex task, where the essential information is distributed among different tabular and list formats - normalized expression values, results from differential expression analysis, and results from functional enrichment analyses. A number of tools and databases are widely used for the purpose of identification of relevant functional patterns, yet often their contextualization within the data and results at hand is not straightforward, especially if these analytic components are not combined together efficiently.ResultsWe developed the GeneTonic software package, whi…