CopyNumber450kCancer 1.0.4 – Baseline Correction for Copy Number Data from Cancer Samples

CopyNumber450kCancer 1.0.4

:: DESCRIPTION

CopyNumber450kCancer takes the output of CopyNumber450k and ChAMP packages and correct the baseline in each sample for accurate copy number calling, specially in cancer samples. CopyNumber450kCancer can read the segment output file from CopyNumber450k package directly without any need for modification. Output files from ChAMP need to be in one file not in seperated files.

::DEVELOPER

Molecular Medicine research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 CopyNumber450kCancer

:: MORE INFORMATION

Citation

CopyNumber450kCancer: Baseline Correction for Accurate Copy Number Calling from the 450k Methylation Array.
Marzouka NA, Nordlund J, Bäcklin CL, Lönnerholm G, Syvänen AC, Almlöf JC.
Bioinformatics. 2015 Nov 9. pii: btv652

BASELINe 1.3 – Bayesian Estimation of Antigen-Driven Selection in Immunoglobulin Sequences

BASELINe 1.3

:: DESCRIPTION

BASELINe, a new computational framework for Bayesian estimation of Antigen-driven selection in Immunoglobulin sequences, provides a more intuitive means of analyzing selection by actually quantifying it.

::DEVELOPER

Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 BASELINe

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Sep 1;40(17):e134. Epub 2012 May 27.
Quantifying selection in high-throughput Immunoglobulin sequencing data sets.
Yaari G1, Uduman M, Kleinstein SH.