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ASCAT
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Serves for dissection of genome-wide allele-specific copy number in tumors. ASCAT infers ASCAT (accurate genome-wide allele-specific copy number) profiles from single nucleotide polymorphism (SNP) array data to evaluate and adjust both tumor cell aneuploidy and non-aberrant cell admixture. The ASCAT profiles generated can be useful for interpretation of cancer genome sequencing data and for identification of changes varying in size from point mutations to complex rearrangements.
HATS / Haplotype Amplification in Tumor Sequences
A tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next-generation sequencing tumor data. The amplified haplotype may reveal gene variants. We assess the performance of HATS using simulated amplified regions generated from varying copy number and coverage levels, followed by amplicons in real data. We demonstrate that HATS infers the amplified alleles more accurately than does the naive approach, especially at low to intermediate coverage levels and in cases (including high coverage) possessing stromal contamination or allelic bias.
FACETS / Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing
Analyzes allele-specific copy number in next generation sequencing (NGS) data. FACETS simplifies systematic identification of clonal and subclonal copy number events through a cellular fraction feature in the model. It can be used for GC-normalization, sequencing bias adjustment and/or segmentation analysis. This tool is useful to simplify large-scale application providing comprehensive output, and integrated visualization.
CalMaTe / Calibration Matrix T
Normalizes allele-specific copy number estimates (ASCNs) from any technology and preprocessing method, without requiring matched normal. CalMaTe is a platform-independent multi-array method that controls single nucleotide polymorphism (SNP)-specific systematic variation by modeling the crosstalk between alleles in bi-allelic SNPs. The software was applied to the TCGA-ovarian cancer dataset. An add-on to the Aroma Project framework is also included in the package.
MARATHON / copy nuMber vARiAtion and Tumor pHylOgeNy
Enables copy number profiling and downstream analyses in disease genetic studies. MARATHON is a pipeline that gathers statistical software: CODEX and CODEX2 perform read depth normalization for total copy number profiling, iCNV receives read depth normalized by CODEX/CODEX2, FALCON and FALCON-X perform allele-specific copy number (ASCN) analysis and Canopy receives input from FALCON/FALCON-X to perform tumor phylogeny reconstruction. The pipeline adapts to different study designs and research goals.
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