The Bioconductor project provides an open resource for the development and distribution of innovative reliable software for computational biology and bioinformatics. The range of available software is broad and rapidly growing as are both the user community and the developer community. The project maintains a web portal for delivering software and documentation to end users as well as an active mailing list. Additional services for developers include a software archive, mailing list and assistance and advice program development and design ? ? We propose an active development strategy designed to meet new challenges while simultaneously providing user and developer support for existing tools and methods. In particular we emphasize a design strategy that accommodates the imperfect, yet evolving nature of biological knowledge and the relatively rapid development of new experimental technologies. Software solutions must be able to rapidly adapt and to facilitate new problems when they arise. ? ?
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| Huber, Wolfgang; Carey, Vincent J; Gentleman, Robert et al. (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods 12:115-21 |
| Lawrence, Michael; Huber, Wolfgang; Pages, Herve et al. (2013) Software for computing and annotating genomic ranges. PLoS Comput Biol 9:e1003118 |
| Gurtowski, James; Schatz, Michael C; Langmead, Ben (2012) Genotyping in the cloud with Crossbow. Curr Protoc Bioinformatics Chapter 15:Unit15.3 |
| Le Meur, Nolwenn; Gentleman, Robert (2012) Analyzing biological data using R: methods for graphs and networks. Methods Mol Biol 804:343-73 |
| Frazee, Alyssa C; Langmead, Ben; Leek, Jeffrey T (2011) ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. BMC Bioinformatics 12:449 |
| Cao, Yi; Yao, Zizhen; Sarkar, Deepayan et al. (2010) Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell 18:662-74 |
| Carvalho, Benilton S; Irizarry, Rafael A (2010) A framework for oligonucleotide microarray preprocessing. Bioinformatics 26:2363-7 |
| Langmead, Ben; Hansen, Kasper D; Leek, Jeffrey T (2010) Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol 11:R83 |
| Langmead, Ben (2010) Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics Chapter 11:Unit 11.7 |
Showing the most recent 10 out of 27 publications
