Dissemination of scientific software with Galaxy ToolShed - PubMed (original) (raw)
- PMID: 25001293
- PMCID: PMC4038738
- DOI: 10.1186/gb4161
Dissemination of scientific software with Galaxy ToolShed
Daniel Blankenberg et al. Genome Biol. 2014.
Abstract
The proliferation of web-based integrative analysis frameworks has enabled users to perform complex analyses directly through the web. Unfortunately, it also revoked the freedom to easily select the most appropriate tools. To address this, we have developed Galaxy ToolShed.
Figures
Figure 1
Frequency of the four possible nucleotides across genomic DNA (accession number SRR345592) and RNA-seq (accession numbers SRR353635-SRR353654) samples for sites 13,636 and 2,619. NVC, Naïve Variant Caller. Data is deposited in the Short Read Archive at the National Center for Biotechnology Information (NCBI).
Similar articles
- deepTools2: a next generation web server for deep-sequencing data analysis.
Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. Ramírez F, et al. Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5. doi: 10.1093/nar/gkw257. Epub 2016 Apr 13. Nucleic Acids Res. 2016. PMID: 27079975 Free PMC article. - Galaxy as a platform for identifying candidate pathogen effectors.
Cock PJ, Pritchard L. Cock PJ, et al. Methods Mol Biol. 2014;1127:3-15. doi: 10.1007/978-1-62703-986-4_1. Methods Mol Biol. 2014. PMID: 24643548 - Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases.
Spoor S, Wytko C, Soto B, Chen M, Almsaeed A, Condon B, Herndon N, Hough H, Jung S, Staton M, Wegrzyn J, Main D, Feltus FA, Ficklin SP. Spoor S, et al. Database (Oxford). 2020 Jan 1;2020:baaa032. doi: 10.1093/database/baaa032. Database (Oxford). 2020. PMID: 32621602 Free PMC article. - Web tools for predictive toxicology model building.
Jeliazkova N. Jeliazkova N. Expert Opin Drug Metab Toxicol. 2012 Jul;8(7):791-801. doi: 10.1517/17425255.2012.685158. Epub 2012 May 12. Expert Opin Drug Metab Toxicol. 2012. PMID: 22577953 Review. - Visualizing protein structures - tools and trends.
Martinez X, Chavent M, Baaden M. Martinez X, et al. Biochem Soc Trans. 2020 Apr 29;48(2):499-506. doi: 10.1042/BST20190621. Biochem Soc Trans. 2020. PMID: 32196545 Review.
Cited by
- Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.
Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. Fungtammasan A, et al. Genome Res. 2015 May;25(5):736-49. doi: 10.1101/gr.185892.114. Epub 2015 Mar 30. Genome Res. 2015. PMID: 25823460 Free PMC article. - Epiviz File Server: Query, transform and interactively explore data from indexed genomic files.
Kancherla J, Yang Y, Chae H, Corrada Bravo H. Kancherla J, et al. Bioinformatics. 2020 Sep 15;36(18):4682-4690. doi: 10.1093/bioinformatics/btaa591. Bioinformatics. 2020. PMID: 32618995 Free PMC article. - Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data.
Cormier MJ, Belyeu JR, Pedersen BS, Brown J, Köster J, Quinlan AR. Cormier MJ, et al. Nat Commun. 2021 Apr 12;12(1):2151. doi: 10.1038/s41467-021-22381-z. Nat Commun. 2021. PMID: 33846313 Free PMC article. - Hybrid male sterility and genome-wide misexpression of male reproductive proteases.
Gomes S, Civetta A. Gomes S, et al. Sci Rep. 2015 Jul 6;5:11976. doi: 10.1038/srep11976. Sci Rep. 2015. PMID: 26146165 Free PMC article. - deepTools2: a next generation web server for deep-sequencing data analysis.
Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. Ramírez F, et al. Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5. doi: 10.1093/nar/gkw257. Epub 2016 Apr 13. Nucleic Acids Res. 2016. PMID: 27079975 Free PMC article.
References
Publication types
MeSH terms
Grants and funding
- HG005133/HG/NHGRI NIH HHS/United States
- R01 HG004909/HG/NHGRI NIH HHS/United States
- HG006620/HG/NHGRI NIH HHS/United States
- HG004909/HG/NHGRI NIH HHS/United States
- T32 GM102057/GM/NIGMS NIH HHS/United States
- U41 HG006620/HG/NHGRI NIH HHS/United States
- HG005542/HG/NHGRI NIH HHS/United States
LinkOut - more resources
Full Text Sources
Other Literature Sources