:: DESCRIPTION
Chi8 is a program that calculates the chi-square 8 degree of freedom test between all pairs of SNPs in a brute force manner on a Graphics Processing Unit.
Usman Roshan
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test.
Al-Jouie A, Esfandiari M, Ramakrishnan S, Roshan U.
BMC Res Notes. 2015 Sep 14;8:436. doi: 10.1186/s13104-015-1392-5.
:: DESCRIPTION
SiGPAT is a useful tool based on gene set analysis for microarray data. It can find significant expression patterns of gene sets by pri-defined biological knowledge. To be unique to other tools, SiGPAT assignes two statistics for each gene sets and classifies expression patterns of gene sets form two dimension distribution of set-level statistics. The tool was evaluated with better performance than current tools such as GSEA and SAM-GS
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The LAMPLINK can detect statistically significant epistatic interactions of two or more SNPs from GWAS data. This software can be used in the same way as the widely used GWAS analysis software PLINK, but LAMPLINK has the additional options for the detection of epistatic interactions with LAMP, which is a multiple testing procedure for combinatorial effects discovery. You can apply LAMPLINK to an analysis pipeline with PLINK simply by replacing plink with lamplink and adding the –lamp option.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
LAMPLINK: detection of statistically significant SNP combinations from GWAS data.
Terada A, Yamada R, Tsuda K, Sese J.
Bioinformatics. 2016 Jul 13. pii: btw418.
:: DESCRIPTION
MultiMotif is a tool for finding statistically significant labeled motifs in multi-relational networks with analytically derived p-values. MultiMotif uses a custom version of RI algorithm for counting occurrences of labeled motifs in a graph and implements an analytical model to assess motifs significance without generating random graphs. MultiMotif works on both directed and undirected networks and handle non-induced labeled motifs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Micale G, Pulvirenti A, Ferro A, Giugno R, Shasha D (2019).
Fast methods for finding significant motifs on labelled multi-relational networks.
Journal of Complex Networks, doi:10.1093/comnet/cnz008
:: DESCRIPTION
LFM-Pro (Local Feature Mining in Proteins) is a framework for automatically discovering family specific local sites and the features associated with these sites.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ahmet Sacan, Ozgur Ozturk, Hakan Ferhatosmanoglu, and Yusu Wang.
LFM-Pro: A Tool for Detecting Significant Local Structural Sites in Proteins.
Bioinformatics, 23(6):709-716, 2007
:: DESCRIPTION
MutSig (for “Mutation Significance”) is a package of tools for analyzing mutation data. It operates on a cohort of patients and identifies mutations, genes, and other genomic elements predicted to be driver candidates. MutSig was developed for the use case of somatic mutations, i.e. mutations that occurred during the development of cancer, and this documentation uses language specific to somatic mutations. However, MutSig has also been used for analysis of germline mutations and is completely applicable to that use case also.
::DEVELOPER
The Cancer Genome Analysis (CGA) group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Shantanu Banerji,et al.
Sequence analysis of mutations and translocations across breast cancer subtypes
Nature 486, 405–409 (21 June 2012) doi:10.1038/nature11154
:: DESCRIPTION
SAIC (Significant Aberrations in Cancer) is a software to identify significant consensus aberrations in cancer genome.
::DEVELOPER
Computational Bioinformatics & Bio-imaging Laboratory (CBIL)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
