Tag: Tumour

CNALR 1.0 – Stratification of Tumour Subtypes based on Copy Number Alteration Profiles

CNALR 1.0

:: DESCRIPTION

CNALR is an R package to perform a stratification of tumour subtypes based on copy number alteration profiles using next-generation sequence data. This webpage is currently set to support the submission of the manuscript Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data

::DEVELOPER

Arief Gusnanto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 CNALR

:: MORE INFORMATION

Citation

Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data.
Gusnanto A, Tcherveniakov P, Shuweihdi F, Samman M, Rabbitts P, Wood HM.
Bioinformatics. 2015 Apr 5. pii: btv191.

ADTEx 2.0 – Aberration Detection in Tumour Exome

ADTEx 2.0

:: DESCRIPTION

ADTEx is a freely available software package coded using R statistical language and Python to detect somatic copy number variations (CNVs) and genotypes in tumour whole exome samples. ADTEx is suitable for paired tumour/matched normal samples.

::DEVELOPER

Kaushalya Amarasinghe <kaushalya.amarasinghe@unimelb.edu.au>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Python
  • BedTOol

:: DOWNLOAD

 ADTEx

:: MORE INFORMATION

Citation:

BMC Genomics. 2014 Aug 28;15:732. doi: 10.1186/1471-2164-15-732.
Inferring copy number and genotype in tumour exome data.
Amarasinghe KC, Li J, Hunter SM, Ryland GL, Cowin PA, Campbell IG, Halgamuge SK

mutationSeq 4.3.9 – Detect Somatic Mutation from Tumour/normal DNA Pair

mutationSeq 4.3.9

:: DESCRIPTION

mutationSeq is a software suite using feature-based classifiers for somatic mutation prediction from paired tumour/normal next-generation sequencing data. mutationSeq has the advantages of integrating different features (e.g., base qualities, mapping qualities, strand bias, and tailed distance features), and validated somatic mutations to make predictions. Given paired normal/tumour bam files, mutationSeq will output the probability of each candidate site being somatic.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 mutationSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 15;28(2):167-75. doi: 10.1093/bioinformatics/btr629.
Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.
Ding J, Bashashati A, Roth A, Oloumi A, Tse K, Zeng T, Haffari G, Hirst M, Marra MA, Condon A, Aparicio S, Shah SP.

ASCAT 2.5.2 – Allele-Specific Copy number Analysis of Tumours

ASCAT 2.5.2

:: DESCRIPTION

ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy.

::DEVELOPER

Peter Van Loo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 ASCAT

:: MORE INFORMATION

Citation:

Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16910-5. doi: 10.1073/pnas.1009843107. Epub 2010 Sep 13.
Allele-specific copy number analysis of tumors.
Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, Perou CM, Børresen-Dale AL, Kristensen VN.

CRImage 1.34.0 – Tumour Image analysis

CRImage 1.34.0

:: DESCRIPTION

CRImage provides image analysis tools for segmentation, classification, and downstream analysis of tumour section images.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

  CRImage

:: MORE INFORMATION

Citation

Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling
Y. Yuan, H. Failmezger, O.M. Rueda, H.R. Ali, S. Gräf, S-F. Chin, R.F. Schwarz, C Curtis, M.J. Dunning, H. Bardwell, N. Johnson, S. Doyle, G. Turashvili, E. Provenzano, S. Aparicio, C. Caldas, F. Markowetz
Science Translational Medicine, 4, 157ra142 (2012)