Files in pkimes/upbm
Tools for the analysis of universal protein binding microarrays
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/AllClasses.R
R/AllGenerics.R
R/PBM-accessors.R
R/PBMDesign-constructor.R
R/PBMDesign-show.R
R/PBMExperiment-constructor.R
R/PBMExperiment-show.R
R/RcppExports.R
R/backgroundSubtract.R
R/checkStratify-helper.R
R/cy3FitEmpirical.R
R/cy3FitModel.R
R/cy3GenerateRef.R
R/cy3Normalize.R
R/fitProbeDistribution.R
R/gpr2PBMExperiment.R
R/kmerFit-estimators.R
R/kmerFit.R
R/kmerTestAffinity.R
R/kmerTestContrast.R
R/kmerTestSpecificity.R
R/mapKmers.R
R/normalizeAcrossReplicates.R
R/normalizeWithinReplicates.R
R/pbmFilterProbes.R
R/pbmTrimProbes.R
R/probeFit.R
R/spatiallyAdjust.R
R/summarizeKmers.R
R/tidy-PBMExperiment.R
R/uniqueKmers.R
R/upbm-package.R
R/upbmPreprocess.R
README.Rmd
README.md
_pkgdown.yml
docs/404.html
docs/LICENSE-text.html
docs/articles/analysis-inference.html
docs/articles/analysis-inference_files/figure-html/difaff-plot-1.png
docs/articles/analysis-inference_files/figure-html/difspec-plot-1.png
docs/articles/analysis-inference_files/figure-html/difspec-plot2-1.png
docs/articles/analysis-inference_files/figure-html/prefaff-plot-1.png
docs/articles/analysis-preprocessing.html
docs/articles/analysis-preprocessing_files/figure-html/bsi-density-1.png
docs/articles/analysis-preprocessing_files/figure-html/cy3-plot-ratios-1.png
docs/articles/analysis-preprocessing_files/figure-html/norm-across-density-1.png
docs/articles/analysis-preprocessing_files/figure-html/norm-within-density-1.png
docs/articles/analysis-preprocessing_files/figure-html/spadj-plot-bias-1.png
docs/articles/analysis-summarization.html
docs/articles/analysis-summarization_files/figure-html/kfit-plot-1.png
docs/articles/analysis-summarization_files/figure-html/kfit-plot-ma-1.png
docs/articles/analysis-summarization_files/figure-html/pfit-plot-1.png
docs/articles/index.html
docs/articles/other-qcplots.html
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-10-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-11-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-13-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-14-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-16-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-17-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-20-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-21-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-24-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-25-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-27-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-28-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-29-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-30-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-5-1.png
docs/articles/other-qcplots_files/figure-html/unnamed-chunk-8-1.png
docs/articles/other-tidydata.html
docs/articles/upbm-classes.html
docs/articles/upbm-preprocessing.html
docs/articles/upbm-preprocessing_files/figure-html/bsi-density-1.png
docs/articles/upbm-preprocessing_files/figure-html/cy3-plot-ratios-1.png
docs/articles/upbm-preprocessing_files/figure-html/norm-across-density-1.png
docs/articles/upbm-preprocessing_files/figure-html/norm-within-density-1.png
docs/articles/upbm-preprocessing_files/figure-html/spadj-plot-bias-1.png
docs/articles/upbm-quickstart.html
docs/articles/upbm-quickstart_files/figure-html/quick-plot-dist-1.png
docs/articles/upbm-quickstart_files/figure-html/quick-plot-ma-1.png
docs/articles/upbm.html
docs/articles/upbm_files/figure-html/quick-plot-res-1.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/PBMDesign-class.html
docs/reference/PBMDesign-replace.html
docs/reference/PBMDesign.html
docs/reference/PBMExperiment-class.html
docs/reference/PBMExperiment.html
docs/reference/PBMclass-accessors.html
docs/reference/backgroundSubtract.html
docs/reference/cy3FitEmpirical.html
docs/reference/cy3FitModel.html
docs/reference/cy3GenerateRef.html
docs/reference/cy3Normalize.html
docs/reference/dl2_estimator.html
docs/reference/dl_estimator.html
docs/reference/figures/upbm.png
docs/reference/fitProbeDistribution.html
docs/reference/gpr2PBMExperiment.html
docs/reference/index.html
docs/reference/kmerFit.html
docs/reference/kmerTestAffinity.html
docs/reference/kmerTestContrast.html
docs/reference/kmerTestSpecificity.html
docs/reference/mapKmers.html
docs/reference/normalizeAcrossReplicates.html
docs/reference/normalizeWithinReplicates.html
docs/reference/pbmFilterProbes.html
docs/reference/pbmTrimProbes.html
docs/reference/probeFit.html
docs/reference/readGPR.html
docs/reference/show-methods.html
docs/reference/spatiallyAdjust.html
docs/reference/summarizeKmers.html
docs/reference/tidy-PBMExperiment.html
docs/reference/tidy-SummarizedExperiment.html
docs/reference/uniqueKmers.html
docs/reference/upbm-package.html
docs/reference/upbmPreprocess.html
man/PBMDesign-class.Rd
man/PBMDesign-replace.Rd
man/PBMDesign.Rd
man/PBMExperiment-class.Rd
man/PBMExperiment.Rd
man/PBMclass-accessors.Rd
man/backgroundSubtract.Rd
man/cy3FitEmpirical.Rd
man/cy3FitModel.Rd
man/cy3GenerateRef.Rd
man/cy3Normalize.Rd
man/dl2_estimator.Rd
man/dl_estimator.Rd
man/figures/upbm.png
man/fitProbeDistribution.Rd
man/gpr2PBMExperiment.Rd
man/kmerFit.Rd
man/kmerTestAffinity.Rd
man/kmerTestContrast.Rd
man/kmerTestSpecificity.Rd
man/mapKmers.Rd
man/normalizeAcrossReplicates.Rd
man/normalizeWithinReplicates.Rd
man/pbmFilterProbes.Rd
man/pbmTrimProbes.Rd
man/probeFit.Rd
man/readGPR.Rd
man/show-methods.Rd
man/spatiallyAdjust.Rd
man/summarizeKmers.Rd
man/tidy-PBMExperiment.Rd
man/tidy-SummarizedExperiment.Rd
man/uniqueKmers.Rd
man/upbm-package.Rd
man/upbmPreprocess.Rd
src/RcppExports.cpp
src/blockmedian.cpp
tests/testthat.R
tests/testthat/test-classes.R
tests/testthat/test-helpers.R
tests/testthat/test-inference.R
tests/testthat/test-preprocessing.R
vignettes/analysis-inference.Rmd
vignettes/analysis-preprocessing.Rmd
vignettes/analysis-summarization.Rmd
vignettes/library.bib
vignettes/other-qcplots.Rmd
vignettes/other-tidydata.Rmd
vignettes/upbm-classes.Rmd
vignettes/upbm-quickstart.Rmd
