ArticleBMC bioinformatics2016
systemPipeR: NGS workflow and report generation environment.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
120 citing papers in PubMed.
- Coordinated regulation of gene expression and microRNA changes in adipose tissue and circulating extracellular vesicles in response to pioglitazone treatment in humans with type 2 diabetes.Frontiers in endocrinology · 2022Trial
- Experimental Acute Exposure to Thirdhand Smoke and Changes in the Human Nasal Epithelial Transcriptome: A Randomized Clinical Trial.JAMA network open · 2019Trial
- Predicting and understanding the response to short-term intensive insulin therapy in people with early type 2 diabetes.Molecular metabolism · 2019Trial
- A Serum lncRNA Signature Determines Oncogenic YAP Activity in Cancer Patients.International journal of cancer · 2026Article
- Simplifying Macroinvertebrate Biodiversity Assessment: A Standardised Metabarcoding Method for Invertebrate Samples With High Volumes of Debris.Molecular ecology resources · 2026Article
- Generation of miR-141/200c conditional knockout mice from knockout-first, reporter-tagged parent and functional validation of the floxed allele.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- systemPipeR: a multipurpose workflow management system for reproducible data analysis.NAR genomics and bioinformatics · 2026Article
- Strawberry Notch 1 Acts as a Transcriptional Regulator Driving Oncogenic Programs in Liver Carcinogenesis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Translational landscape during seed germination revealed by ribosome profiling.The Plant journal : for cell and molecular biology · 2026Article
- CHIP-seq and transcriptomics reveal a new role of circadian-regulated StBBX24 protein in potato reproduction.BMC plant biology · 2025Article
- Genetic and epigenetic markers in the METTL21C gene associated with umbilical hernia in pigs.BMC genomics · 2025Article
- mRNA turnover dynamics are affected by cell differentiation and loss of the cytosine methyltransferase Nsun2.Nucleic acids research · 2025Article
- Decay drives RNA abundance regulation using three distinct regulatory mechanisms.bioRxiv : the preprint server for biology · 2025Article
- Regulation of lung cancer initiation and progression by the stem cell determinant Musashi.eLife · 2025Article
- Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function.BMC genomics · 2024Article
- Comprehensive genomic features indicative for Notch responsiveness.Nucleic acids research · 2024Article
- An in vitro neurogenetics platform for precision disease modeling in the mouse.Science advances · 2024Article
- A massive alteration of gene expression in undescended testicles of dogs and the association ofProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Riboseq-flow: A streamlined, reliable pipeline for ribosome profiling data analysis and quality control.Wellcome open research · 2024Article
- Chromosome 8p engineering reveals increased metastatic potential targetable by patient-specific synthetic lethality in liver cancer.Science advances · 2023Article
60 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
backgroundNext-generation sequencing (NGS) has revolutionized how research is carried out in many areas of biology and medicine. However, the analysis of NGS data remains a major obstacle to the efficient utilization of the technology, as it requires complex multi-step processing of big data demanding considerable computational expertise from users. While substantial effort has been invested on the development of software dedicated to the individual analysis steps of NGS experiments, insufficient resources are currently available for integrating the individual software components within the widely used R/Bioconductor environment into automated workflows capable of running the analysis of most types of NGS applications from start-to-finish in a time-efficient and reproducible manner.
resultsTo address this need, we have developed the R/Bioconductor package systemPipeR. It is an extensible environment for both building and running end-to-end analysis workflows with automated report generation for a wide range of NGS applications. Its unique features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software on local computers and computer clusters. A flexible sample annotation infrastructure efficiently handles complex sample sets and experimental designs. To simplify the analysis of widely used NGS applications, the package provides pre-configured workflows and reporting templates for RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Additional workflow templates will be provided in the future.
conclusionssystemPipeR accelerates the extraction of reproducible analysis results from NGS experiments. By combining the capabilities of many R/Bioconductor and command-line tools, it makes efficient use of existing software resources without limiting the user to a set of predefined methods or environments. systemPipeR is freely available for all common operating systems from Bioconductor ( http://bioconductor.org/packages/devel/systemPipeR ).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.