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The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data

Robert Petryszak, Nuno A Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y Amy Tang, Alvis Brazma, Bonnie Berger
2017 Bioinformatics  
We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near  ...  Availability and Implementation: The RNASeq-er API can be accessed at  ...  the Ensembl and WormBase ParaSite teams for facilitating timely access to the genome references; the ENA Team for their assistance in retrieval the raw RNA-Seq data; and finally to the Samples, Phenotypes  ... 
doi:10.1093/bioinformatics/btx143 pmid:28369191 pmcid:PMC5870697 fatcat:ild6vn5ll5hcfj4alj5kksj234

recount3: summaries and queries for large-scale RNA-seq expression and splicing [article]

Christopher Wilks, Shijie C. Zheng, Feng Yong Chen, Rone Charles, Brad Solomon, Jonathan P. Ling, Eddie Luidy Imada, David Zhang, Lance Joseph, Jeffrey T. Leek, Andrew E. Jaffe, Abhinav Nellore (+3 others)
2021 bioRxiv   pre-print
We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline.  ...  Taken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio  ...  Acknowledgements Funding: CW, BL, KDH, SCJ, FYC, RC, BS, JTL, AN, LCT were supported by R01GM121459 to KDH. CW, RC, BS and BL were supported by R01GM118568 and R35GM139602 to BL. DZ is  ... 
doi:10.1101/2021.05.21.445138 fatcat:hee4epm6f5dpfmygt5u7yyfwca

Human genome meeting 2016

A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson, R. Polimanti, J. Gelernter, X. Lin (+828 others)
2016 Human Genomics  
Further, targeted quantitative analysis of a subset of discriminating metabolites using tandem mass spectrometry provided a reliable laboratory method to detect children with ASD.  ...  analysis.  ...  Acknowledgements Funding for research and development is acknowledged for Project: "Research Oriented Data Management and Analysis" at the Ucar Lab by The Jackson Laboratory, USA.  ... 
doi:10.1186/s40246-016-0063-5 pmid:27294413 pmcid:PMC4896275 fatcat:ycjj53ixrbauvnusibuz76y7bm

Data Analysis for the COVID-19 Research: Contributions of the German Network of Bioinformatics Infrastructure

Alfred Pühler
2021
In total, there are 15 projects showing how different de.NBI resources can be used in the analysis of large data sets.  ...  Finally, a pre sentation of the federated de.NBI Cloud  ...  GALAXY AS A GATEWAY FOR DATA ANALYSIS The European Galaxy platform (https:// usegalaxy.eu) serves as a gateway for data analysis and access to databases for scientists of all disciplines.  ... 
doi:10.4119/unibi/2950259 fatcat:d5f5slq25vabtieou4pzpbr75e