BEclear 2.8.0 – Batch Effect Detection and Adjustment in DNA Methylation Data

BEclear 2.8.0

:: DESCRIPTION

BEclear enables researchers to identify those portions of the data that deviate statistically significant from the remaining data and to replace these portions by typical values reconstructed from neighboring data entries based on latent factor models.

::DEVELOPER

Chair of Computational Biology at the Saarland University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

BEclear

:: MORE INFORMATION

Citation

Akulenko R, Merl M, Helms V.
BEclear: Batch Effect Detection and Adjustment in DNA Methylation Data.
PLoS One. 2016 Aug 25;11(8):e0159921. doi: 10.1371/journal.pone.0159921. PMID: 27559732; PMCID: PMC4999208.

P_ACT 1.2 – P-values: Adjustment for Correlated Tests

P_ACT 1.2

:: DESCRIPTION

p_ACT (P-values: Adjustment for Correlated Tests) is an R program that adjusts sets of up to 500 p-values from association tests between correlated traits and SNPs for multiple testing, accounting for the correlation between tests.

::DEVELOPER

Center for Statistical Genetics, University of Michigan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 P_ACT

:: MORE INFORMATION

Citation

Conneely, K.N. and Boehnke, M. (2007)
So many correlated tests, so little time! Rapid adjustment of p-values for multiple correlated tests.
American Journal of Human Genetics 81:1158-1168.

DWD – Perform Systematic Bias Adjustment in microarray data.

DWD

:: DESCRIPTION

DWD (Distance Weighted Discrimination) can perform systematic bias adjustment in microarray data.

::DEVELOPER

Dr. J. S. Marron in the Department of Statistics at University of North Carolina at Chapel Hill.

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 DWD

:: MORE INFORMATION

Citation

Adjustment of Systematic Microarray Data Biases.
M. Benito, J. Parker, Q. Du, J. Wu, D. Xiang, C. Perou, J. Marron
Bioinformatics 20:105-144, 2004