:: DESCRIPTION
LRMotifs is a novel method of DNA sequence motif discovery based on logistic regression and rigorous hypothesis testing.
::DEVELOPER
David M Simcha dsimcha@gmail.com
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2012;7(11):e47836. doi: 10.1371/journal.pone.0047836. Epub 2012 Nov 7.
The limits of de novo DNA motif discovery.
Simcha D1, Price ND, Geman D.
:: DESCRIPTION
Comrad is a novel algorithmic framework for the integrated analysis of RNA-Seq and Whole Genome Shotgun Sequencing (WGSS) data for the purposes of discovering genomic rearrangements and aberrant transcripts. The Comrad framework leverages the advantages of both RNA-Seq and WGSS data, providing accurate classification of rearrangements as expressed or not expressed and accurate classification of the genomic or non-genomic origin of aberrant transcripts.
::DEVELOPER
Lab for Bioinformatics and Computational Genomics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Andrew McPherson, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach1, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins and S. Cenk Sahinalp
Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data
Bioinformatics (2011)doi: 10.1093/bioinformatics/btr184
:: DESCRIPTION
Heinz is a tool for single-species active module discovery.
xHeinz is a software solver that searches for active subnetwork modules that are conserved between two species. It uses a branch-and-cut algorithm that finds provably optimal or near-optimal solutions.
::DEVELOPER
Algorithmic Bioinformatics, Heinrich-Heine-Universität Düsseldorf
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
xHeinz: An algorithm for mining cross-species network modules under a flexible conservation model.
El-Kebir M, Soueidan H, Hume T, Beisser D, Dittrich M, Müller T, Blin G, Heringa J, Nikolski M, Wessels LF, Klau GW.
Bioinformatics. 2015 May 27. pii: btv316
:: DESCRIPTION
GRAM (Genetic RegulAtory Modules) identifies modules, collections of genes that share common regulators as well as expression profiles.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nat Biotechnol. 2003 Nov;21(11):1337-42. Epub 2003 Oct 12.
Computational discovery of gene modules and regulatory networks.
Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.
:: DESCRIPTION
VISDA (VIsual and Statistical Data Analyzer) is a software for cluster modeling, visualization, and discovery in genomic data. VISDA performs progressive, coarse-to-fine (divisive) hierarchical clustering and visualization, supported by hierarchical mixture modeling, supervised/unsupervised informative gene selection, supervised/unsupervised data visualization, and user/prior knowledge guidance, to discover hidden clusters within complex, high-dimensional genomic data.
::DEVELOPER
Computational Bioinformatics & Bio-imaging Laboratory (CBIL)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
caBIG VISDA: modeling, visualization, and discovery for cluster analysis of genomic data.
Zhu Y, Li H, Miller DJ, Wang Z, Xuan J, Clarke R, Hoffman EP, Wang Y.
BMC Bioinformatics. 2008 Sep 18;9:383.
:: DESCRIPTION
GeneProgram is a new unsupervised computational framework based on Hierarchical Dirichlet Processes that addresses each of the above challenges. GeneProgram uses expression data to simultaneously organize tissues into groups and genes into overlapping programs with consistent temporal behavior, to produce maps of expression programs, which are sorted by generality scores that exploit the automatically learned groupings.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS Comput Biol. 2007 Aug;3(8):e148. Epub 2007 Jun 13.
Automated discovery of functional generality of human gene expression programs.
Gerber GK, Dowell RD, Jaakkola TS, Gifford DK.
:: DESCRIPTION
laSV is a software that employs a local de novo assembly based approach to detect genomic structural variations from whole-genome high-throughput sequencing datasets.
::DEVELOPER
ZLab, University of Massachusetts Medical School, Worcester, MA, USA
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2015 Sep 30;43(17):8146-56. doi: 10.1093/nar/gkv831. Epub 2015 Aug 17.
Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes.
Zhuang J, Weng Z
:: DESCRIPTION
PTRStalker is a new algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences.
DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ab initio detection of fuzzy amino acid tandem repeats in protein sequences
Marco Pellegrini, M. Elena Renda, Alessio Vecchio
BMC Bioinformatics 2012, Vol. 13(Suppl 3):S8, March 2012.
:: DESCRIPTION
Lumpy is a new probabilistic framework that we have developed to integrate multiple structural variation signals such as discordant paired-end alignments and split-read alignments. While it is clear that integrating all SV signals is important for sensitive discovery, most existing (including our own Hydra) tools only exploit one signal. Lumpy integrates multiple signals in order to improve sensitivity and breakpoint resolution. This is especially important for cancer genome analysis where tumor heterogeneity causes potentially important rearrangements occur with less supporting alignments in the sampled DNA.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Layer RM, Quinlan AR, Hall IM,
LUMPY: A probabilistic framework for structural variant discovery.
arXiv:1210.2342v2 [q-bio.GN]
:: DESCRIPTION
Hydra detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose “signatures” corroborate the same putative breakpoint. Hydra can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments.
Hydra-Multi is a paired-end read structural variant discovery tool that is capable of integrating signals from hundreds of samples.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Population-based structural variation discovery with Hydra-Multi.
Lindberg MR, Hall IM, Quinlan AR.
Bioinformatics. 2014 Dec 2. pii: btu771.
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
Aaron R. Quinlan1, Royden A. Clark1, Svetlana Sokolova1, Mitchell L. Leibowitz1, Yujun Zhang2, Matthew E. Hurles2, Joshua C. Mell3 and Ira M. Hall
Genome Res. 2010. 20: 623-635
