Tag: SLR

SLR 0.1.9 – Performing Smoothed Logistic Regression for CGH data

SLR 0.1.9

:: DESCRIPTION

SLR is a software of fitting smoothed logistic regression with Cauchy-Normal Random Probes Effects with application to aCGH data

::DEVELOPER

Huang Jian <j.huang@ucc.ie> , Prof. Yudi Pawitan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux /MacOsX
  • R package

:: DOWNLOAD

 SLR

:: MORE INFORMATION

Citation

Stat Med. 2009 Dec 30;28(30):3798-810. doi: 10.1002/sim.3753.
Classification of array CGH data using smoothed logistic regression model.
Huang J1, Salim A, Lei K, O’Sullivan K, Pawitan Y.

SLR 1.4.3 – Sitewise Likehood Ratio Estimation of Selection

SLR 1.4.3

:: DESCRIPTION

SLR (Sitewise Likehood Ratio) is a program to detect sites in coding DNA that are unusually conserved and/or unusually variable (that is, evolving under purify or positive selection) by analysing the pattern of changes for an alignment of sequences on an evolutionary tree. The strength of selection at each site is determined by comparing the rate of nonsynonymous (amino acid changing) substitutions to that of synonymous (silent) substituions, the latter assumed to be invisible to selection and so evolving in a strictly neutral fashion.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 SLR

:: MORE INFORMATION

Citation:

Genetics. 2005 Mar;169(3):1753-62. Epub 2005 Jan 16.
Detecting amino acid sites under positive selection and purifying selection.
Massingham T, Goldman N.