:: DESCRIPTION
PriorityPruner is a software program which can prune a list of SNPs that are in high linkage disequilibrium (LD) with other SNPs in the list, while preferentially keeping/selecting SNPs of higher priority (e.g., the most significant SNPs in a genome-wide association study).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The SNPsnap webserver enables SNP-based enrichment analysis by providing matched sets of SNPs that can be used to calibrate background expectations.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
SNPsnap: a web-based tool for identification and annotation of matched SNPs.
Pers TH, Timshel P, Hirschhorn JN.
Bioinformatics. 2014 Oct 13. pii: btu655.
:: DESCRIPTION
LDsplit is an open source Java program that detects SNPs (single nulceotide polymorphisms) associated with meiotic recombination hotspots.
::DEVELOPER
Jie Zheng, Ph.D.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms.
Yang P, Wu M, Guo J, Kwoh CK, Przytycka TM, Zheng J.
BMC Bioinformatics. 2014 Feb 17;15:48. doi: 10.1186/1471-2105-15-48.
:: DESCRIPTION
SNPHunter: Searches an alignment file (e.g. AceParser output) for SNPs using multiple parameters and filters (works with AssemblyFilter) for quality, homopolymer runs, and alternative splicing/assembly error. Options to include Blast annotation and ORF information for codon position and synonomous/nonsynonymous amino acid changes and to generate population specific output.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MultAssoc is a MATLAB software package for test of association of a disease with a group of SNPs after accounting for their interaction with another group of SNPs or environmental exposures. In addition to implementing two standard logistic regression based tests, the package implements a novel method, called TukAssoc, that uses the Tukey’s 1 d.f. model for interaction between two groups of covariates.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chatterjee N., Kalaylioglu Z., Moslehi R., Peters U., Wacholder S. (2006).
Powerful multilocus tests of genetic association in the presence of gene-gene and gene-environment interactions.
American Journal of Human Genetics, Vol. 79, 1002-16.
:: DESCRIPTION
Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
::DEVELOPER
Genome Analysis Toolbox with de-Bruijn graph (GATB)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Ecol Resour. 2014 Mar;14(2):393-400. doi: 10.1111/1755-0998.12179. Epub 2013 Nov 11.
Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms.
Quillery E1, Quenez O, Peterlongo P, Plantard O.
:: DESCRIPTION
FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs.
Coetzee SG, Rhie SK, Berman BP, Coetzee GA, Noushmehr H.
Nucleic Acids Res. 2012 Oct;40(18):e139. doi: 10.1093/nar/gks542.
:: 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
JEPEG is a novel software which uses only summary statistics and correlation structures estimated from a reference popluation, to i) impute the summary statistics at unmeasured eQTLs and ii) test for the joint effect of measured and imputed all eQTLs affecting a gene function/expression on a phenotype.
JEPEGMIX is a JEPEG extension for gene-level joint testing of functional variants.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts.
Lee D, Williamson VS, Bigdeli TB, Riley BP, Webb BT, Fanous AH, Kendler KS, Vladimirov VI, Bacanu SA.
Bioinformatics. 2015 Oct 1. pii: btv567
JEPEG: a summary statistics based tool for gene-level joint testing of functional variants.
Lee D, Williamson VS, Bigdeli TB, Riley BP, Fanous AH, Vladimirov VI, Bacanu SA.
Bioinformatics. 2014 Dec 12. pii: btu816
:: DESCRIPTION
PinSnps is an interactive tool for the analysis of common variants, disease-related single-nucleotide polymorphisms (SNPs), Post-Translational Modifications (PTMs) and related functional sites mapped onto human protein interaction networks. One can search for and retrieve information about SNPs data and interacting proteins of the query.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Lu HC, Herrera Braga J, Fraternali F.
PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks.
Bioinformatics. 2016 Aug 15;32(16):2534-6. doi: 10.1093/bioinformatics/btw153. Epub 2016 Mar 24. PMID: 27153707; PMCID: PMC4978923.