Harman: The removal of batch effects from datasets using a PCA and constrained optimisation based technique

Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.

AuthorJosh Bowden [aut], Jason Ross [aut, cre], Yalchin Oytam [aut]
Date of publicationNone
MaintainerJason Ross <jason.ross@csiro.au>
LicenseGPL-3 + file LICENCE
Version1.2.0
http://www.bioinformatics.csiro.au/harman/

View on Bioconductor

Files

Harman/DESCRIPTION
Harman/Harman.Rproj
Harman/LICENCE
Harman/NAMESPACE
Harman/R
Harman/R/Harman.R Harman/R/arrowPlot.R Harman/R/callHarman.R Harman/R/detachHarman.R Harman/R/harmanScores.R Harman/R/harmanresults.R Harman/R/pcaPlot.R Harman/R/plot.harmanresults.R Harman/R/prcompPlot.R Harman/R/reconstructData.R Harman/R/shiftBetas.R Harman/R/summary.harmanresults.R Harman/R/zzz.R
Harman/README.md
Harman/build
Harman/build/vignette.rds
Harman/inst
Harman/inst/CITATION
Harman/inst/NEWS.Rd
Harman/inst/doc
Harman/inst/doc/IntroductionToHarman.R
Harman/inst/doc/IntroductionToHarman.Rmd
Harman/inst/doc/IntroductionToHarman.html
Harman/inst/extdata
Harman/inst/extdata/NPM_data_first_1000_rows.csv.gz
Harman/inst/extdata/NPM_info.csv.gz
Harman/inst/unitTests
Harman/inst/unitTests/test_R_layer.R
Harman/inst/unitTests/test_Rcpp_layer.R
Harman/man
Harman/man/arrowPlot.Rd Harman/man/callHarman.Rd Harman/man/detachHarman.Rd Harman/man/harman.Rd Harman/man/harmanScores.Rd Harman/man/harmanresults.Rd Harman/man/pcaPlot.Rd Harman/man/plot.harmanresults.Rd Harman/man/prcompPlot.Rd Harman/man/print.summary.harmanresults.Rd Harman/man/reconstructData.Rd Harman/man/shiftBetas.Rd Harman/man/summary.harmanresults.Rd
Harman/src
Harman/src/CMapSelectKFromN.h
Harman/src/CSelectRandom.h
Harman/src/Harman.cpp
Harman/src/Makevars
Harman/src/Makevars.win
Harman/tests
Harman/tests/runTests.R
Harman/vignettes
Harman/vignettes/IntroductionToHarman.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.