Bioconductor: open software development for computational biology and bioinformatics
- PMID: 15461798
- PMCID: PMC545600
- DOI: 10.1186/gb-2004-5-10-r80
Bioconductor: open software development for computational biology and bioinformatics
Abstract
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.
Figures
Similar articles
-
CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications.BMC Bioinformatics. 2024 Mar 12;25(1):110. doi: 10.1186/s12859-024-05695-9. BMC Bioinformatics. 2024. PMID: 38475691 Free PMC article.
-
Tools and collaborative environments for bioinformatics research.Brief Bioinform. 2011 Nov;12(6):549-61. doi: 10.1093/bib/bbr055. Epub 2011 Oct 7. Brief Bioinform. 2011. PMID: 21984743 Free PMC article.
-
Bioconductor: an open source framework for bioinformatics and computational biology.Methods Enzymol. 2006;411:119-34. doi: 10.1016/S0076-6879(06)11008-3. Methods Enzymol. 2006. PMID: 16939789 Review.
-
arrayQualityMetrics--a bioconductor package for quality assessment of microarray data.Bioinformatics. 2009 Feb 1;25(3):415-6. doi: 10.1093/bioinformatics/btn647. Epub 2008 Dec 23. Bioinformatics. 2009. PMID: 19106121 Free PMC article.
-
Using R and Bioconductor in Clinical Genomics and Transcriptomics.J Mol Diagn. 2020 Jan;22(1):3-20. doi: 10.1016/j.jmoldx.2019.08.006. Epub 2019 Oct 9. J Mol Diagn. 2020. PMID: 31605800 Review.
Cited by
-
Relationship of MicroRNA according to Immune Components of Breast Milk in Korean Lactating Mothers.Pediatr Gastroenterol Hepatol Nutr. 2024 Sep;27(5):322-331. doi: 10.5223/pghn.2024.27.5.322. Epub 2024 Sep 9. Pediatr Gastroenterol Hepatol Nutr. 2024. PMID: 39319280 Free PMC article.
-
Protocol to infer and analyze miRNA sponge modules in heterogeneous data using miRSM 2.0.STAR Protoc. 2024 Sep 17;5(4):103317. doi: 10.1016/j.xpro.2024.103317. Online ahead of print. STAR Protoc. 2024. PMID: 39292559 Free PMC article.
-
Atomic vacancies of molybdenum disulfide nanoparticles stimulate mitochondrial biogenesis.Nat Commun. 2024 Sep 17;15(1):8136. doi: 10.1038/s41467-024-52276-8. Nat Commun. 2024. PMID: 39289340 Free PMC article.
-
RAD52 resolves transcription-replication conflicts to mitigate R-loop induced genome instability.Nat Commun. 2024 Sep 5;15(1):7776. doi: 10.1038/s41467-024-51784-x. Nat Commun. 2024. PMID: 39237529 Free PMC article.
-
Molecular and biochemical components associated with chilling tolerance in tomato: comparison of different developmental stages.Mol Hortic. 2024 Sep 5;4(1):31. doi: 10.1186/s43897-024-00108-0. Mol Hortic. 2024. PMID: 39232835 Free PMC article.
References
-
- Bioconductor http://www.bioconductor.org
-
- GNU operating system - Free Software Foundation http://www.gnu.org
-
- Dafermos GN. Management and virtual decentralised networks: The Linux project. First Monday. 2001;6(11) http://www.firstmonday.org/issues/issue6_11/dafermos/index.html
-
- Free Software Project Management HOWTO http://www.tldp.org/HOWTO/Software-Proj-Mgmt-HOWTO
-
- Torvalds L. The Linux edge. Comm Assoc Comput Machinery. 1999;42:38–39. doi: 10.1145/299157.299165. - DOI
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources