:: DESCRIPTION
GLFD is an exploratory data analysis method. Its purpose is to find latent factors that act in combination with clinical factors to control feature expression.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Genomics. 2011 Nov 16;12:563. doi: 10.1186/1471-2164-12-563.
Improving gene expression data interpretation by finding latent factors that co-regulate gene modules with clinical factors.
Yu T, Bai Y.
:: DESCRIPTION
kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome.
Gardner SN, Slezak T, Hall BG.
Bioinformatics. 2015 Sep 1;31(17):2877-8. doi: 10.1093/bioinformatics/btv271.
PLoS One. 2013 Dec 9;8(12):e81760. doi: 10.1371/journal.pone.0081760. eCollection 2013.
When whole-genome alignments just won’t work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes.
Gardner SN, Hall BG.
:: DESCRIPTION
integron_gene_fetch is developed to get integron genes from metagenomic sequencing reads. It is capable of getting the integron mobile genes more efficiently, as these genes are extremely difficult to be detected in whole-genome assembly. By assembling the dataset and traces all potential paths between any two contigs that consist of recombination sites, the integron_gene_fetch tool is able to get more integron genes given a pre-determined set of recombination site sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yu-Wei Wu, Mina Rho, Thomas G. Doak and Yuzhen Ye.
Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes.
Appl. Environ. Microbiol. August 2012 vol. 78 no. 15 5288-5296
:: DESCRIPTION
RetroSeq is a tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available.
::DEVELOPER
Genomics & Genetics At The Sanger Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
RetroSeq: transposable element discovery from next-generation sequencing data
Thomas M. Keane, Kim Wong and David J. Adams
Bioinformatics (2013) 29 (3): 389-390.
:: DESCRIPTION
SamCluster is an integrated scheme and corresponding program for automatic discovery of sample classes based on gene expression profile.
::DEVELOPER
Center of Computational Biology, Beijing Institute of Basic Medical Sciences
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2003 May 1;19(7):811-7.
SamCluster: an integrated scheme for automatic discovery of sample classes using gene expression profile.
Li W, Fan M, Xiong M.
:: DESCRIPTION
GeneTerrain is a next-generation panel biomarker discovery and validation software.
::DEVELOPER
Discovery Informatics and Computing Laboratory@ Indiana University School of Informatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
Please join the mailing group to obtain instructions for downloading a pre-release version of the software.
:: MORE INFORMATION
Citation
You Qian, Shiaofen Fang, and Jake Y. Chen (2008)
GeneTerrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks
Information Visualization, doi: 10.1057/palgrave.ivs.9500169
:: DESCRIPTION
NMF (Non-negative Matrix Factorization), an algorithm based on decomposition-by-parts, recovers meaningful information without supervision. Coupled with a novel model selection mechanism, and efficiently implemented in Matlab, NMF is a powerful method for identification of context-dependent patterns in complex biological systems.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jean-Philippe Brunet, Pablo Tamayo, Todd Golub, Jill Mesirov
Metagenes and molecular pattern discovery using matrix factorization
Proc. Natl. Acad. Sci. USA 2004 101: 4164-4169
:: DESCRIPTION
BreakPtr (abbrev. for Break-Pointer) is a computational approach for segmenting CGH data and analyzing chromosomal DNA sequence. Its Finder predicts breakpoints of large deletions and amplifications. Its Annotator identifies actual dosage ratios.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Korbel JO, Urban AE, Grubert F, Du J, Royce TE, Starr P, Zhong, G, Emanuel BS, Weissman SM, Snyder M & Gerstein MB (2007)
Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome,
PNAS June 12, 2007 vol. 104 no. 24 10110-10115
:: DESCRIPTION
DASS (Discovery of All Significant Substructures) that first identifies all substructures in unordered data (DASSSub) in a manner that is especially efficient for modular data. In addition, DASS calculates the statistical significance of the identified substructures, for sets with at most one element of each type (DASSPset), or for sets with multiple occurrence of elements (DASSPmset).
::DEVELOPER
Dr. Maik Friedel , J.Hollunder
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
DASS: Efficient Discovery and P-Value Calculation of Substructures in Unordered Data
Jens Hollunder, Maik Friedel, Andreas Beyer, Christopher T. Workman, Thomas Wilhelm
Bioinformatics (2007), 23(1): 77-83.
:: DESCRIPTION
The mosclust R package (that stands for model order selection for clustering problems) implements a set of functions to discover significant structures in bio-molecular data. One of the main problems in unsupervised clustering analysis is the assessment of the “natural” number of clusters. Several methods and software tools have been proposed to tackle this problem
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2007 Feb 1;23(3):387-9. Epub 2006 Nov 24.
Mosclust: a software library for discovering significant structures in bio-molecular data.
Valentini G.