Identifies tumor genomes using data from single nucleotide polymorphism (SNP) microarrays. hapLOH detects subtle allelic imbalance and low proportions of cells harboring aberrant allelic ratio among non-aberrant cells, in unpaired tumor samples using SNP microarrays. This software is appropriate to use in the presence of high levels of germline contamination.
Permits analysis of high-density tiling microarray data. tilingArray is based on a confidence interval estimation model. It can be used to identify the boundary, structure and level of coding and non-coding transcripts of yeast. This tool can be useful in the study of transcriptional complexity under dynamic conditions and in other organisms and for the application of tiling arrays in the detection of genomic regions purified in chromatin-immunoprecipitation experiments.
Provides functions for finding complement, reverse and mismatch sequences and for counting nucleotide content. matchprobes contains fast algorithms for string and regular expression matching, for reversing sequences and for obtaining complementary sequences. There is a fast string matching function that searches for matches of the probe sequences on the microarray to a query sequence which may, e.g. represent a transcript of interest.
Automates the detection of long-range linkage disequilibrium (LD) regions and removes them. bigsnpr is designed for analysis of single nucleotide polymorphism (SNP) arrays. It discards SNPs in long-range LD regions for the human genome regions before computing principal components (PCs). This tool is useful for increasing statistical power of a genome wide association study (GWAS).
Allows users to discover recurrent loss-of-heterozygosity (LOH) from single nucleotide polymorphism (SNP) genotypes. HWELOH is a R package, using the Hardy–Weinberg equilibrium principle, developed for identifying LOH in both hemizygous deletion and copy-neutral LOH as well as detecting regions that contains important tumor-suppressor genes, without relying on matched normal genotype data.
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.
Provides a data management and interpretation software. QSNPlite simplifies systematic PLACE-SSCP (Single-Strand Conformation Polymorphism) analysis of individual and pooled DNAs, incorporating quantitative interpretation of SSCP in capillary array (QUISCA). It can also process the data from the sequencing analysis to identify the single nucleotide polymorphism (SNP) nucleotides of the alleles detected by SSCP.
Assists in enabling high throughput analysis. FlexiChip is a Zip-code array that be used to test any single nucleotide polymorphisms (SNP). It is also adaptable to large scale studies to validate new molecular marker candidates.
Allows users to identify the copy numbers of single nucleotide polymorphisms (SNPs) alleles and parental chromosomes in cancer cells from SNP array data. PLASQ is a R package, a generalized linear model, that allows to deduce allele-specific copy number (ASCN) and parent-specific copy number (PSCN). It was tested on (SNP) array data from 12 lung cancer samples.
Serves for clustering DNA features by using array comparative genomic hybridization (arrayCGH) data from tumor samples. dnaCplusT executes dimension reduction through two separated steps: collapsing and clustering. The fast collapsing is on all array features whereas the model-based clustering is done on the resulting regions. It uses a stability score and a cross-validation to evaluate the randomness of the clustering result.
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.
Executes hypothesis testing for array comparative genomic hybridization (arrayCGH) regions based on calls. CGHtest contains several functions to conduct hypothesis tests: Wilcoxon-Mann-Whitney two-sample test, Kruskal-Wallis k-sample test, chi-square association test, binomial proportion test and multiple comparisons. Entire set of tests performed are utilized to calculate false discovery rates (FDR).
A package that provides an extension of the RangedSummarizedExperiment class with additional API features. This class provides convenient and fast methods for working with segmented genomic data. Additionally, GenoSet provides the class RleDataFrame which stores runs of data along the genome for multiple samples and provides very fast summaries of arbitrary row sets (regions of the genome).
A set of tools for lossless compression of microarray images, however, MENT can be used in other kind of images such as medical, RNAi, etc. This set of tools is divided into two categories, defined by the decomposition approach used: Bitplane Decomposition or Binary-Tree Decomposition.
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.
This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.
Provides data structures for representing enhanced suffix arrays. Libfid is a portable software library for accessing indexed data and implements many functions frequently performed on these data, such as reading indexed data from files, and for performing common operations such as fast string matching. This resource comes with its own enhanced suffix array construction program.
Provides annotation information to probe sequences. ProbeLynx compares the input sequences against genomic sequence data and gene predictions for seven different species. The application detects probe targets by performing a sequence similarity analysis coupled to a cross-hybridization filtering. Then, users have the possibility to choose among different annotation types which to attach to their set. The software is a part of ArrayPipe.
Identifies runs of shared homozygosity (ROSHs). KinSNP is a software for homozygosity mapping in single nucleotide polymorphism (SNP) arrays from consanguineous families. It was designed to mimic the data processing strategy traditionally used by geneticists to manually locate homozygous regions in microsatellite-based data. It can also serve as a starting point for further microsatellite-based fine mapping of candidate regions using classical linkage analysis.
Evaluates genotyping performance. SXTestPlate was developed for the statistical analysis of a test run. The software reports the call rate and concordance for each DNA of the test plate and each single nucleotide polymorphism (SNP) of the control pool. It automatically determines how often a sample is replicated, by grouping the imported genotypes by identical DNA and SNP identifiers. SXTestPlate can be used independently of the Applied Biosystems test kits.
Improves GeneMapper analysis. GMFilter has been developed as a Windows program for the automated filtering of SNPlex raw data. The software automatically removes bad wells (corresponding to bad samples) from the raw data reduces noise, which improves the analysis. It needs about 10 minutes for processing the sample plot table of a 384-well plate on a normal desktop computer.
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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