Tag: CNA

OncodriveCIS 1.1.0 – Assesses the Influence of Copy Number Alterations (CNA) in the Gene Expression

OncodriveCIS 1.1.0

:: DESCRIPTION

OncodriveCIS  is a method to identify genes that accumulate copy number alterations important for tumour development. This is done by computing the functional impact of CNAs by measuring their effect on the expression of the genes affected.

::DEVELOPER

 The Biomedical Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 OncodriveCIS

:: MORE INFORMATION

Citation

Tamborero D, Lopez-Bigas N and Gonzalez-Perez A.
Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression.
PLoS ONE 8(2): e55489. doi:10.1371/journal.pone.0055489

TitanCNA v1.17.1 – Analysis of subClonal CNA and LOH in Cancer

TitanCNA v1.17.1

:: DESCRIPTION

TitanCNA is a R/Bioconductor package for analyzing subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in whole genome and exome sequencing of tumours.

::DEVELOPER

The Ha Lab @FredHutch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

TitanCNA

:: MORE INFORMATION

Citation

Ha, G., et al. (2014).
TITAN: Inference of copy number architectures in clonal cell populations from tumour whole genome sequence data.
Genome Research, 24: 1881-1893. (PMID: 25060187)

CNAnorm 1.39.0 – Estimate Copy Number Aberrations (CNA) in Cancer Samples

CNAnorm 1.39.0

:: DESCRIPTION

CNAnorm is an R package to perform normalisation of copy number from next generation sequence data, taking into account tumour cell content and possible aneuploid genome size.

::DEVELOPER

the LICP Pre-Cancer Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R package
  • Bioconductor

:: DOWNLOAD

 CNAnorm

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 1;28(1):40-7. doi: 10.1093/bioinformatics/btr593. Epub 2011 Oct 28.
Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data.
Gusnanto A, Wood HM, Pawitan Y, Rabbitts P, Berri S.

SynthEx 1.05 – CNA detection and Tumor Heterogeneity profiling

SynthEx 1.05

:: DESCRIPTION

SynthEx is a comprehensive suite of tools for CNA detection and tumor heterogeneity profiling. It is tailored to cater for the multiple characteristics of different next generation sequencing technologies.

::DEVELOPER

Chen Group at U Chicago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • R 

:: DOWNLOAD

SynthEx

:: MORE INFORMATION

Citation

Silva GO, Siegel MB, Mose LE, Parker JS, Sun W, Perou CM, Chen M.
SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.
Genome Biol. 2017 Apr 8;18(1):66. doi: 10.1186/s13059-017-1193-3. PMID: 28390427; PMCID: PMC5385048.

VisualCNA 1.0 – Constraint Network Analysis and Protein Engineering

VisualCNA 1.0

:: DESCRIPTION

VisualCNA is a PyMOL plug-in for interactive Constraint Network Analysis and protein engineering for improving thermostability

::DEVELOPER

the Gohlke Group

:: SCREENSHOTS

VisualCNA

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python
  • PyMOL

:: DOWNLOAD

 VisualCNA

:: MORE INFORMATION

Citation

VisualCNA: A GUI for interactive Constraint Network Analysis and protein engineering for improving thermostability.
Rathi PC, Mulnaes D, Gohlke H.
Bioinformatics. 2015 Mar 12. pii: btv139.

CRP_CNV – Conditional Random Pattern Model for Copy Number Aberration (CNA) Detection

CRP_CNV

:: DESCRIPTION

CRP_CNV is a conditional random pattern (CRP) model for CNA detection where much contextual cues are explored to suppress the noise and improve CNA detection accuracy.

::DEVELOPER

Center for Bioinformatics & Systems Biology, The Methodist Hospital Research Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CRP_CNV

:: MORE INFORMATION

Citation

Li, F, Zhou, X., Huang, WT, Wong STC, Chang CC,
Conditional Random Pattern Model for Copy Number Aberration Detection,
BMC Bioinformatics, 11:200, 2010