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aCGH and SNP microarray software tools

Microarray software tools

aCGH and SNP microarray applications

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aCGH and SNP microarray workflow schema

Array comparative genomic hybridization (aCGH; Pinkel et al., 1998) and single nucleotide polymorphism (SNP) microarray (Mei et al., 2000) are array-based karyotyping techniques which can help determine the genome abnormalities causing genetic disorders and the acquired genome copy number changes in cancer cells (Attiyeh et al., 2009; Chen et al., 2011). Both array CGH and SNP genotyping are routinely utilized by clinicians for the evaluation of patients with developmental delay, multiple congenital anomalies (Stankiewicz and Beaudet, 2007) and neuropsychiatric disorders (Lupski, 2012).

Most Recent Tools

new
OMIC_12619
CNV detection

pennCNV_Pipeline

A quality score for copy number variants (CNVs) detected by PennCNV, prior to performing…

A quality score for copy number variants (CNVs) detected by PennCNV, prior to performing CNV-based association studies. Our contribution can be viewed as a post-processing step of PennCNV calls, whereby various CNV metrics are combined to estimate…

new
OMIC_12299
Oligonucleotide design

Re-Annotator

A re-annotation pipeline for microarray probe sequences. The Re-Annotator is primarily…

A re-annotation pipeline for microarray probe sequences. The Re-Annotator is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays. It uses a custom-built mRNA reference database to identify the…

new
OMIC_12116
Data import

compendiumdb

Provides an environment for downloading functional genomics data from Gene Expression…

Provides an environment for downloading functional genomics data from Gene Expression Omnibus (GEO), parsing the information into a local or remote database, and interacting with the database using dedicated R functions, thus enabling seamless…

new
OMIC_11873
Chromothripsis-like pattern…

CTLPScanner

A web server for detection of chromothripsis-like pattern (CTLP) in genomic array data.…

A web server for detection of chromothripsis-like pattern (CTLP) in genomic array data. CTLPScanner consists of two main modules: (i) detection and visualization of chromothripsis, and annotation of the detected chromosome pulverization region and…

Most Popular Tools

popular
OMIC_02570
Somatic CNA detection

ASCAT

A tool for accurate dissection of genome-wide allele-specific copy number in tumors.

A tool for accurate dissection of genome-wide allele-specific copy number in tumors.

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