Tag: Graphical Model

JointSNVMix 0.8.0 – Graphical Model to Analyse Sequence Data from Tumour/normal Pairs

JointSNVMix 0.8.0

:: DESCRIPTION

JointSNVMix implements a probabilistic graphical model to analyse sequence data from tumour/normal pairs. The model draws statistical strength by analysing both genome jointly to more accurately classify germline and somatic mutations.The JointSnvMix software package consists of a number of tools for calling somatic mutations in tumour/normal paired NGS data.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 JointSNVMix

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Apr 1;28(7):907-13. doi: 10.1093/bioinformatics/bts053. Epub 2012 Jan 27.
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.
Roth A1, Ding J, Morin R, Crisan A, Ha G, Giuliany R, Bashashati A, Hirst M, Turashvili G, Oloumi A, Marra MA, Aparicio S, Shah SP.

FastGGM 20151105 – Algorithm for the inference of Gaussian Graphical Model in Biological Networks

FastGGM 20151105

:: DESCRIPTION

FastGGM is an R package for efficiently studying conditional dependence among variables, which is well known as the Gaussian graphical model (GGM).

::DEVELOPER

Chen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
:: DOWNLOAD

 FastGGM

:: MORE INFORMATION

Citation

Wang T, Ren Z, Ding Y, Fang Z, Sun Z, MacDonald ML, Sweet RA, Wang J, Chen W.
FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks.
PLoS Comput Biol. 2016 Feb 12;12(2):e1004755. doi: 10.1371/journal.pcbi.1004755. PMID: 26872036; PMCID: PMC4752261.