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CNVtools
A statistical framework for performing case-control CNV association studies that applies likelihood ratio testing of quantitative CNV measurements in cases and controls. CNVtools can model large batch effects that do not follow group membership, which is an important consideration in large-scale association studies. It is based on methods that are robust to differential errors and noisy data and can achieve maximal theoretical power. CNVtools‘ computational efficiency is such that it would be feasible to use this software to test for CNV associations genome-wide (>10,000 loci).
SNPExpress
Enables, in a combinatorial way, the analysis of single nucleotide polymorphism (SNP) genotype calls, copy numbers, polymorphic copy number variations (CNVs) and gene expression. SNPExpress is available for use with Affymetrix DNA mapping arrays, Illumina HumanHap550 Genotyping BeadChip and Affymetrix GeneChips. The software facilitates the identification of biologically and clinically relevant entities. It can be useful to genome-wide studies by providing an integrated view of data from DNA mapping and mRNA expression arrays.
DMET-Miner / Drug Metabolism Enzyme and Transporters-Miner
Enables the read of data produced by the Affymetrix DMET platform and to extract relevant knowledge by computing frequent item sets. DMET-Miner is based on two main steps: (1) transformation of a DMET dataset into a transaction database; and (2) learning of significant rules from the transaction database by mining frequent item sets. Moreover, this tool is able to correlate a single variant for each probe (related to a portion of a gene).
R-Gada
Integrates: (i) data import from most common formats of Affymetrix, Illumina and aCGH arrays; (ii) a fast and accurate segmentation algorithm to call CNVs based on Genome Alteration Detection Analysis (GADA); and (iii) functions for displaying and exporting the Copy Number calls, identification of recurrent CNVs, multivariate analysis of population structure, and tools for performing association studies. The package provides the tools for creating a complete integrated pipeline from data normalization to statistical association. It can efficiently handle a massive volume of data consisting of millions of genetic markers and hundreds or thousands of samples with very accurate results.
DMET-Analyzer
A tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The proposed system allows: (i) to automatize the workflow of analysis of DMET-SNP data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaGKB, a major knowledge base for pharmacogenomic studies. DMET-Analyzer has a simple graphical user interface that allows users (doctors/biologists) to upload and analyse DMET files produced by Affymetrix DMET-Console in an interactive way.
GWCNV
Detects CNV associations with diseases through a genome-wide algorithm. GWCNV is a genome-wide algorithm for detecting CNV associations with diseases. It works directly on a transformation of intensity data. It is powerful and sensitive in detecting small CNV associations, and retains high power for large CNVs. Users should first run a modified version of PennCNV, which is included in the GWCNV package, to generate the input file that contains all the defined probabilities at each SNP. After running GWCNV, the association test results for different copy numbers at each SNP are reported in the output file specified by users.
PedCNV
Provides two methods for association study: first, the observed probe intensity measurement can be directly used to detect the association of copy number variation (CNV) with phenotypes of interest, and second, provides an implementation for association analysis with CNV data in R. Also, the most probable copy number is estimated with the proposed likelihood and the association of the most probable copy number with phenotype is tested. This method can be applied to both the independent and correlated population.
MinorityReport
Facilitates the comparison of any two sets of genome alignments for the purpose of rapidly identifying the spectrum of nonsynonymous changes, insertions or deletions. MinoritReport also copies number variations in a presumed mutant relative to its parent. It relates mapped sequence reads in SAM format output from any alignment tool for both the mutant and parent genome, relative to a reference genome, and produces the set of variants that distinguishes the mutant from the parent, all presented in an intuitive, straightforward report format.
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