Difference between revisions of "CEQer"
(Created page with "{{Bioinformatics application |sw summary=CEQer (Comparative Exome Quantification analyzer) is a graphical, event-driven tool for copy number abnormalities/allelic-imbalance co...") |
Janazuczkova (talk | contribs) |
||
| (4 intermediate revisions by 4 users not shown) | |||
| Line 1: | Line 1: | ||
{{Bioinformatics application | {{Bioinformatics application | ||
| − | |sw summary=CEQer (Comparative Exome Quantification analyzer) is a graphical, event-driven tool for copy number abnormalities/allelic-imbalance coupled analysis of whole-exome sequencing data. By using case-control matched exome data, CEQer performs a comparative digital exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance detection. | + | |sw summary=CEQer (Comparative Exome Quantification analyzer) is a graphical, event-driven tool for copy number abnormalities/allelic-imbalance coupled analysis of whole-exome sequencing data. By using case-control matched exome data, CEQer performs a comparative digital exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance detection. |
|sw logo=CEQer.jpeg | |sw logo=CEQer.jpeg | ||
| − | |bio domain=Exome analysis, | + | |bio domain=Exome analysis, Copy number estimation, Genetic variation analysis |
| − | |||
|bio tech=Any | |bio tech=Any | ||
| + | |interface=Command line, | ||
| + | |resource type=Command-line tool, | ||
|created by=Piazza Rocco | |created by=Piazza Rocco | ||
| − | |created at=University of Milano-Bicocca, | + | |created at=University of Milano-Bicocca, |
|maintained=Yes | |maintained=Yes | ||
|email address=rocco.piazza@unimib.it | |email address=rocco.piazza@unimib.it | ||
| + | |input format=SAM/BAM, Pileup | ||
| + | |output format=Graphical | ||
| + | |sw feature=Copy number and allelic imbalance analyses from matched exomes. | ||
| + | |language=C# | ||
| + | |licence=GPLv3 | ||
| + | |os=Windows, Mac, Linux | ||
}} | }} | ||
== Description == | == Description == | ||
<!-- Describe the application in the space below --> | <!-- Describe the application in the space below --> | ||
| − | + | Copy number alterations (CNA) are common events occurring in leukaemias and solid tumors. Comparative Genome Hybridization (CGH) is actually the gold standard technique to analyze CNAs; however, CGH analysis requires dedicated instruments and is able to perform only low resolution Loss of Heterozygosity (LOH) analyses. CEQer (Comparative Exome Quantification analyzer) is a graphical, event-driven tool for CNA/allelic-imbalance (AI) coupled analysis of exome sequencing data. By using case-control matched exome data, CEQer performs a comparative digital exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance detection. This data is used to build mixed statistical/heuristic models allowing the identification of CNA/AI events. | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
<!-- --> | <!-- --> | ||
Latest revision as of 11:32, 3 November 2016
|
Application data |
|
| Created by | Piazza Rocco |
|---|---|
| Biological application domain(s) | Exome analysis, Copy number estimation, Genetic variation analysis |
| Technology | Any |
| Created at | University of Milano-Bicocca |
| Maintained? | Yes |
| Input format(s) | SAM/BAM, Pileup |
| Output format(s) | Graphical |
| Software features | Copy number and allelic imbalance analyses from matched exomes. |
| Programming language(s) | C# |
| Interface type(s) | Command line |
| Resource type(s) | Command-line tool |
| Licence | GPLv3 |
| Operating system(s) | Windows, Mac, Linux |
| Contact: | rocco.piazza@unimib.it |
Summary: CEQer (Comparative Exome Quantification analyzer) is a graphical, event-driven tool for copy number abnormalities/allelic-imbalance coupled analysis of whole-exome sequencing data. By using case-control matched exome data, CEQer performs a comparative digital exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance detection. 200px|right
"Error: no local variable "counter" was set." is not a number.
Description
Copy number alterations (CNA) are common events occurring in leukaemias and solid tumors. Comparative Genome Hybridization (CGH) is actually the gold standard technique to analyze CNAs; however, CGH analysis requires dedicated instruments and is able to perform only low resolution Loss of Heterozygosity (LOH) analyses. CEQer (Comparative Exome Quantification analyzer) is a graphical, event-driven tool for CNA/allelic-imbalance (AI) coupled analysis of exome sequencing data. By using case-control matched exome data, CEQer performs a comparative digital exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance detection. This data is used to build mixed statistical/heuristic models allowing the identification of CNA/AI events.
Links
References
To add a reference for CEQer, enter the PubMed ID in the field below and click 'Add'.
Search for "CEQer" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
