0000000000042707

AUTHOR

Jan Linke

showing 3 related works from this author

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…

QH301-705.5Process (engineering)Computer scienceShinyComputer applications to medicine. Medical informaticsBioconductor610 MedizinR858-859.7Context (language use)Interactive data analysisReproducible researchBioconductorInteractivity610 Medical sciencesUse caseRNA-SeqBiology (General)MIT LicenseTranscriptomicsInformation retrievalBase SequenceSequence Analysis RNAData interpretationData visualizationRReproducibility of ResultsIdentification (information)WorkflowRNASoftwareFunctional enrichment analysis
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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…

Differential expression analysisComputer scienceShinyBioconductorInteractive data analysislcsh:Computer applications to medicine. Medical informaticsReproducible researchBioconductorDifferential expressionCode (cryptography)Transcriptome profilingHumansRNA-SeqTranscriptomicslcsh:QH301-705.5Flexibility (engineering)Ideal (set theory)Base Sequencebusiness.industryData visualizationGene Expression ProfilingRRNAReproducibility of ResultsTransparency (human–computer interaction)Gene Expression Regulationlcsh:Biology (General)Data Interpretation StatisticalWeb applicationlcsh:R858-859.7Software engineeringbusinessSoftwareBMC Bioinformatics
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Common miRNA Patterns of Alzheimer's Disease and Parkinson's Disease and Their Putative Impact on Commensal Gut Microbiota.

2019

With the rise of Next-Generation-Sequencing (NGS) methods, Micro-RNAs (miRNAs) have achieved an important position in the research landscape and have been found to present valuable diagnostic tools in various diseases such as multiple sclerosis or lung cancer. There is also emerging evidence that miRNAs play an important role in the pathogenesis of neurodegenerative diseases such as Alzheimer’s disease (AD) or Parkinson’s disease (PD). Apparently, these diseases come along with changes in miRNA expression patterns which led to attempts from researchers to use these small RNA species from several body fluids for a better diagnosis and in order to observe disease progression. Additionally, it…

610 Medical sciencesmicro-RNAsneurodegenerationParkinson’s disease610 Medizingut microbiomeAlzheimer’s diseaselcsh:Neurosciences. Biological psychiatry. NeuropsychiatryNeuroscienceOriginal Researchcrosstalklcsh:RC321-571Frontiers in neuroscience
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