Bioconductor Project

Sandrine Dudoit is a Core Developer of the Bioconductor Project, an open-source and open-development software project for the analysis of biomedical and genomic data.

The following are software packages authored by group members.

• affxparser: Affymetrix file parsing SDK. H. Bengtsson, J. Bullard, R. Gentleman, K. D. Hansen, and M. Morgan. (Bioconductor Project)
• biomaRt: Interface to BioMart databases (e.g., Ensembl, COSMIC, Wormbase, and Gramene). S. Durinck and W. Huber. (Bioconductor Project)
• cosmo: Supervised detection of conserved motifs in DNA sequences (COnstrained Search for MOtifs). O. Bembom, F. Gallusser, and S. Dudoit. (Bioconductor Project; cosmo Project)
• cosmoGUI: GUI for constructing constraint sets used by the cosmo package. F. Gallusser, O. Bembom, and S. Dudoit. (Bioconductor Project; cosmo Project)
• DEGraph: Two-sample tests on a graph. L. Jacob, P. Neuvial, and S. Dudoit. (Bioconductor Project)
• EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq. D. Risso and S. Dudoit. (Bioconductor Project)
• GenomeGraphs: Plotting genomic information from Ensembl. S. Durinck and J. Bullard. (Bioconductor Project)
• Genominator: Tools for storing, accessing, visualizing, and analyzing genomic data; SQLite database. J. Bullard and K. D. Hansen. (Bioconductor Project)
• marray: Exploratory analysis for two-color spotted microarray data (classes and methods, diagnostic plots, normalization procedures, quality assessment). Y. H. Yang, with contributions from A. Paquet and S. Dudoit. (Bioconductor Project)
• multtest: Resampling-based multiple hypothesis testing. K. S. Pollard, H. N. Gilbert, Y. Ge, S. Taylor, and S. Dudoit. (Bioconductor Project)
• seqLogo: Sequence logos for DNA sequence alignments. O. Bembom. (Bioconductor Project; cosmo Project)
• sma: Statistical microarray analysis. S. Dudoit, Y. H. Yang, and B. M. Bolstad, with contributions from N. Thorne, I. Lonnstedt, and J. Mar. (CRAN)

Bioconductor Project Working Papers Series.