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DR_SEQAN / Drug Resistance SEQuence ANalyzer
Provides expert advice on human immunodeficiency virus (HIV) genotypic resistance interpretation. DR_SEQAN identifies mutations in the reverse transcriptase (RT)- and protease (PR)-coding regions of the HIV-1 genome. It integrates an interpretation algorithm to predict viral drug susceptibility. In addition, this application provides a report with published phenotypic data for mutations or combinations of mutations found in the query sequence.
BeadDataPackR
A package based on a compression scheme for raw Illumina BeadArray data, designed to ease the burdens of sharing and storing such data. BeadDataPackR offers two key advantages over off-the-peg compression tools. First it uses knowledge of the data formats to achieve greater compression than other approaches, and second it does not need to be decompressed for analysis, but rather the values held within can be directly accessed. BeadDataPackR provides two functions. The function compressBeadData() takes the raw files and produces a .babfile from them, while the function decompress- BeadData() takes a .bab file and reconstructs the .txt and .locsfiles to the requested degree of precision. While the ability to reconstruct the original files is useful, given that many existing analysis scripts may expect the raw files, this step is not a necessity. Indeed, the structure of the file format means data can be extracted directly, allowing it to form the primary input to analysis tools.
aCGH
Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. These latter represent batch of arrays of Comparative Genomic Hybridization data. In addition to that, there are slots for representing phenotype and various genomic events associated with aCGH experiments, such as transitions, amplifications, aberrations, and whole chromosomal gains and losses.
Seq4SNPs
Obsolete
Allows human single nucleotide polymorphism (SNP) assay sequence preparation. Seq4SNPs is a web-based, walk-away software, available with adjacent SNP addition for human SNPs. The software delivers multiple sequences suited to genotyping assay designers, that are annotated with adjacent SNPs. It has been used in the Taqman and SNPstream workflow, as well as for fasta retrieval for other bioinformatics tests and to determine the chromosome and position of a SNP given the Reference SNP ID (dbSNP) (rs) number.
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