Software
Sandrine Dudoit is a founding core developer of the Bioconductor Project (http://www.bioconductor.org), an opensource and opendevelopment 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, J. Hester, and M. Morgan.
R package: [Bioconductor]

biomaRt:
Interface to BioMart databases (e.g. Ensembl, COSMIC, Wormbase and Gramene).
S. Durinck and W. Huber.
R package: [Bioconductor]

clusterExperiment: Resamplingbased sequential ensemble clustering.
E. Purdom, R. Risso, and M. Johnson.
R package: [Bioconductor]

cosmo:
Supervised detection of conserved motifs in DNA sequences (COnstrained Search for MOtifs).
O. Bembom, F. Gallusser, and S. Dudoit.
R package: [Bioconductor]

cosmoGUI:
GUI for constructing constraint sets used by the cosmo package.
F. Gallusser, O. Bembom, and S. Dudoit.
R package: [Bioconductor]

DEGraph:
Twosample tests on a graph.
L. Jacob, P. Neuvial, and S. Dudoit.
R package: [Bioconductor]

EDASeq:
Exploratory data analysis and normalization for RNASeq.
D. Risso, S. Dudoit, and L. Geistlinger.
R package: [Bioconductor]

GenomeGraphs:
Plotting genomic information from Ensembl.
S. Durinck and J. Bullard.
R package: [Bioconductor]

Genominator:
Analyze, manage and store genomic data.
J. Bullard and K. D. Hansen.
R package: [Bioconductor]

marray:
Exploratory analysis for twocolor spotted microarray data (classes and methods, data input, diagnostic plots, normalization procedures, quality assessment).
Y. H. Yang, with contributions from A. Paquet and S. Dudoit.
R package: [Bioconductor]

multtest:
Resamplingbased multiple hypothesis testing.
K. S. Pollard, H. N. Gilbert, Y. Ge, S. Taylor, and S. Dudoit.
R package: [Bioconductor]

RUVSeq:
Remove unwanted variation from RNASeq data.
D. Risso, S. Dudoit, L. Pantano, and K. Slowikowski.
R package: [Bioconductor]

scone:
Single Cell Overview of Normalized Expression data.
M. Cole and D. Rissso.
R package: [Bioconductor]

seqLogo:
Sequence logos for DNA sequence alignments.
O. Bembom.
R package: [Bioconductor]

slingshot: Tools for ordering singlecell sequencing.
K. Street.
R package: [Bioconductor]

sma:
Statistical microarray analysis.
S. Dudoit, Y. H. Yang, and B. M. Bolstad, with contributions from N. Thorne, I. Lonnstedt, and J. Mar.

zinbwave:
ZeroInflated Negative Binomialbased Wanted Variation Extraction (ZINBWaVE).
D. Risso, S. Gribkova, and J.P. Vert.
R package: [Bioconductor]