ArticlePloS one2013
GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing.International journal of molecular sciences · 2020Article
- Tacrolimus rescues the signaling and gene expression signature of endothelial ALK1 loss-of-function and improves HHT vascular pathology.Human molecular genetics · 2017Article
- A mouse model of hereditary hemorrhagic telangiectasia generated by transmammary-delivered immunoblocking of BMP9 and BMP10.Scientific reports · 2016Article
- Exome Sequencing and Prediction of Long-Term Kidney Allograft Function.PLoS computational biology · 2016Article
- Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution.Journal of visualized experiments : JoVE · 2015Article
- Methods of integrating data to uncover genotype-phenotype interactions.Nature reviews. Genetics · 2015Review
- Altered histone mark deposition and DNA methylation at homeobox genes in human oral squamous cell carcinoma.Journal of cellular physiology · 2014Article
- Growth of the developing cerebral cortex is controlled by microRNA-7 through the p53 pathway.Cell reports · 2014Article
- Altered epigenetic regulation of homeobox genes in human oral squamous cell carcinoma cells.Experimental cell research · 2014Article
- Article
- Tmem88a mediates GATA-dependent specification of cardiomyocyte progenitors by restricting WNT signaling.Development (Cambridge, England) · 2013Article
- Activation of HIF2α in kidney proximal tubule cells causes abnormal glycogen deposition but not tumorigenesis.Cancer research · 2013Article
- Compression of structured high-throughput sequencing data.PloS one · 2013Article
- GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data.PloS one · 2013Article
- HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads.Journal of the American Medical Informatics Association : JAMIAArticle
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
We present GobyWeb, a web-based system that facilitates the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension mechanism. Analyses currently supported include quantification of gene expression for messenger and small RNA sequencing, estimation of DNA methylation (i.e., reduced bisulfite sequencing and whole genome methyl-seq), or the detection of pathogens in sequenced data. In contrast to previous analysis pipelines developed for analysis of HTS data, GobyWeb requires significantly less storage space, runs analyses efficiently on a parallel grid, scales gracefully to process tens or hundreds of multi-gigabyte samples, yet can be used effectively by researchers who are comfortable using a web browser. We conducted performance evaluations of the software and found it to either outperform or have similar performance to analysis programs developed for specialized analyses of HTS data. We found that most biologists who took a one-hour GobyWeb training session were readily able to analyze RNA-Seq data with state of the art analysis tools. GobyWeb can be obtained at http://gobyweb.campagnelab.org and is freely available for non-commercial use. GobyWeb plugins are distributed in source code and licensed under the open source LGPL3 license to facilitate code inspection, reuse and independent extensions http://github.com/CampagneLaboratory/gobyweb2-plugins.
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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.