Search Results for "snp" - Page 4
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Showing 96 open source projects for "snp"
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Genovar is a JAVA-based stand alone software in order to detect unknown genomic variants, analyze SNP-related copy number variant regions, and comprehensively visualize genomic data such as array CGH and sequence alignments results.
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An analysis pipeline for mining exome-Seq and RNA-Seq data, focusing on quality control, SNP identification and annotation, RNA quantification, differentially expressed genes analysis, eqtl, and pathway analysis. http://seqgene.sourceforge.net
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MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.
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CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
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Utility to convert PED genome file into RAW SNP format. Creates multiple files per person. Supports big files. The same conversion utility has been included into "aisconvert" toolkit, so this project is rather deprecated.
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Genevar (GENe Expression VARiation) is a platform of database and web services for the integrative analysis and visulization of SNP-gene assocaitaions in eQTL studies.
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A collection of applications for epistatic detection in genome-wide data. With user-provided genotype and phenotype data, as well as a few parameters, the applications are able to return the significant SNP-pairs.
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The SNP ratio test can assess significance of enrichment of significant associations in genome-wide association studies. Tests can be applied to pathways such as KEGG/GO, or user-defined pathways to test specific hypotheses. See link below for more.
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Avenzoar is a one-year exploration of renal cell carcinoma morphology and its related single nucleotide polymorphisms (SNPa) as a method of automating diagnosis of cancer by using a computer-aided decision tree controlled by analytical statistics.
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This is a Perl module for doing snp analysis based on shotgun sequencing reads and a reference genome sequence. Its primary input is the cigar alignment format outputted from ssaha2.
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The annotation files for Illumina SNP genotyping platforms generated for performing Homozygosity Haplotype analysis
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This software implements a method we recently developed (ADT) that analyzes cancer SNP array data in a novel manner to detect nucleotide alleles and haplotypes selected for amplification in recurrently amplified regions across tumors samples.
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openADAM is a web-based database management system for the large amount of genotype data generated from the Affymetrix GeneChip® Mapping Array and Genome-Wide Human SNP Array platforms
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A program to model HapMap haplotypes in genetic association studies using tag SNP genotypes. Please visit http://www.ucd.ie/genepi/hapmixmap for more details.
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SNPMATIC (SNP MicroArray Training, Inference and Classification) is a tool for SNP genotype analysis of Affymetrix SNP Microarrays. It is in the early stages of development and it is expected that interest will be limited mainly to developers for now.
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MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition A genetic algorithm for generating SNP tiling paths from a large SNP database based on the competing objectives of cost (number of SNPs) and coverage (haplotype blocks): Hubley R., Zitzler
