Please see also the software collection of the Centre for Bioinformatics and our GitHub repository.
ASCAT
Supplement to the paper Allele-specific copy number analysis of tumors (Peter Van Loo, Silje H. Nordgard, Ole Christian Lingjærde, Hege G. Russnes, Inga H. Rye, Wei Sun, Victor J. Weigman, Peter Marynen, Anders Zetterberg, Bjørn Naume, Charles M. Perou, Anne-Lise Børresen-Dale, Vessela N. Kristensen, Proceedings of the National Academy of Sciences 2010) [link to paper]
CARMA
Supplement to the paper "DNA copy number motifs are strong and independent predictors of survival in breast cancer" by Arne Pladsen et al. (2020).
clusterGenomics
Supplement to the paper Identifying clusters in genomics data by recursive partitioning (Gro Nilsen, Knut Liestøl, Ørnulf Borgan and Ole Christian Lingjærde; Journal of Statistical Applications in Genetics and Molecular Biology 2013; In Press).
Comparison of platforms for classification of copy number alterations
Supplement to the paper Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors (Baumbusch, Aarøe, Johansen, Hicks, Sun, Bruhn, Gunderson, Naume, Kristensen, Liestøl, Børresen-Dale and Lingjærde, BMC Genomics 2008, 9:379; doi:10.1186/1471-2164-9-379) [link to paper]
Copynumber
Software accompanying the paper Copynumber: Efficient algorithms for single- and multi-track copy number segmentation (Gro Nilsen, Knut Liestøl, Peter Van Loo, Hans Kristian Moen Vollan, Marianne B Eide, Oscar M Rueda, Suet-Feung Chin, Roslin Russell, Lars O Baumbusch, Carlos Caldas, Anne-Lise Børresen-Dale and Ole Christian Lingjærde, BMC Genomics, 2012, 13:591) [link to paper]
Estimating the number of clusters in a data set (ERA)
Supplement to the master thesis A comparative study of existing and novel methods for estimating the number of clusters in a data set (Gro Nilsen, March 2009). [link to thesis]
Genome Architecture
Supplementary material for the paper: Genomic architecture characterizes tumor progression paths and fate in breast cancer patients (Hege G. Russnes, Hans Kristian Moen Vollan, Ole Christian Lingjærde, Alexander Krasnitz, Pär Lundin, Bjørn Naume, Therese Sørlie, Elin Borgen, Inga H. Rye, Anita Langerød, Suet-Feung Chin, Andrew E. Teschendorff, Philip J. Stephens, Susanne Månér, Ellen Schlichting, Lars O. Baumbusch, Rolf Kåresen, Michael P. Stratton, Michael Wigler, Carlos Caldas, Anders Zetterberg, James Hicks, Anne-Lise Børresen-Dale, Science Translational Medicine, 2010) [link to paper]
Genomic Hyperbrowser
Statistical methodology and computing power to handle a variety of biological inquires on genomic datasets. See the paper: The Genomic HyperBrowser: inferential genomics at the sequence level (Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestol K, Clancy T, Ferkingstad E, Johansen M, Nygaard V, Tostesen E, Frigessi A, Hovig E. Genome Biology 2010, 11(12):R121. PubMed PMID: 21182759) [link to paper]
PARALIGN
Search tool described in the paper PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology (Sæbø;, Andersen, Myrseth, Lærdahl and Rognes, Nucleic Acids Research , 33, W535-539, 2005) [link to paper]
PLS-Cox for genome-wide data
Software for the paper Partial least squares Cox regression for genome-wide data (Nygård, Borgan, Størvold and Lingjærde, Lifetime Data Analysis, 2008; doi: 10.1007/s10985-007-9076-7) [link to abstract]
RNAmmer
Tool described in the paper RNammer: consistent annotation of rRNA genes in genomic sequences (Lagesen, Hallin, Rødland, Stærfeldt, Rognes, Ussery, Nucleic Acids Research, 35, 3100-3108, 2007) [link to paper]
SWARM
Tool described in the paper Swarm: robust and fast clustering method for amplicon-based studies. (Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. (2014), PeerJ 2:e593) [link to paper]
SWIPE
Search tool described in the paper Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation (Rognes, BMC Bioinformatics 12, 221, 2011) [link to paper]
Survival Prediction with Microarrays
Software for the paper Predicting survival from microarray data - a comparative study (Bøvelstad, Nygård, Størvold, Aldrin, Borgan, Frigessi and Lingjærde, Bioinformatics 2007) [link to paper]
VSEARCH
Software described in the following paper:
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584. doi: 10.7717/peerj.2584