Files in jvanheld/stats4bioinfo
Utilities for the book "Statistics for bioinformatics"
.gitignore
DESCRIPTION
NAMESPACE
R/ROCstatistics.R
R/VolcanoPlot.R
R/featureColors.R
R/heatmap.simple.R
R/kmerFrequenciesToMarkov.R
R/meanEqualityTests.R
R/meanEqualityTests.compareTwoTests.R
R/meanEqualityTests.plotVolcano.R
R/multipleTestingCorrections.R
R/multipleTestingCorrections.plotCorrectedVsPval.R
R/multipleTestingCorrections.plotPvalDistrib.R
R/multipleTestingCorrections.plotSignifFeatures.R
R/plot.ROC.R
R/plot.ROC.R~
R/plotPvalCompa.R
R/plotROCframe.R
R/plotROCfromFiles.R
R/plotROCfromFiles.R~
R/randIndexDetailed.R
R/rnormPerGroup.R
R/rowwisePermGroupBalanced.R
R/rowwiseRandomNormal.R
R/rowwiseSample.R
R/seqToPSSM.R
R/stats4bioinfo.R
R/statsPerRow.R
R/stderPlot.R
R/tTestPerRow.R
R/tTestPerRow.bootstrap.R
R/tTestPerRow.bootstrap.VolcanoBoxPlot.R
R/tTestPerRow.bootstrap.hist.R
R/tTestPerRow.plotVolcano.R
R/util.R
R/wilcoxTestPerRow.R
README.md
Read-and-delete-me
Rmd/.gitignore
Rmd/robust_estimators_Samuel_Grandjeau_2015-04.Rmd
Rmd/robust_estimators_Venet_Brohee.Rmd
inst/extdata/markov_models/Arabidopsis_thaliana_TAIR10/1nt_genomic_Arabidopsis_thaliana_TAIR10-1str-ovlp.freq.gz
inst/extdata/markov_models/Arabidopsis_thaliana_TAIR10/1nt_genomic_Arabidopsis_thaliana_TAIR10-1str-ovlp_transitions.tab
inst/extdata/markov_models/Arabidopsis_thaliana_TAIR10/1nt_genomic_Arabidopsis_thaliana_TAIR10-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Arabidopsis_thaliana_TAIR10/2nt_genomic_Arabidopsis_thaliana_TAIR10-1str-ovlp.freq.gz
inst/extdata/markov_models/Arabidopsis_thaliana_TAIR10/2nt_genomic_Arabidopsis_thaliana_TAIR10-1str-ovlp_transitions.tab
inst/extdata/markov_models/Arabidopsis_thaliana_TAIR10/2nt_genomic_Arabidopsis_thaliana_TAIR10-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Arabidopsis_thaliana_TAIR10/3nt_genomic_Arabidopsis_thaliana_TAIR10-1str-ovlp.freq.gz
inst/extdata/markov_models/Arabidopsis_thaliana_TAIR10/3nt_genomic_Arabidopsis_thaliana_TAIR10-1str-ovlp_transitions.tab
inst/extdata/markov_models/Arabidopsis_thaliana_TAIR10/3nt_genomic_Arabidopsis_thaliana_TAIR10-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Arabidopsis_thaliana_TAIR10/4nt_genomic_Arabidopsis_thaliana_TAIR10-1str-ovlp.freq.gz
inst/extdata/markov_models/Arabidopsis_thaliana_TAIR10/4nt_genomic_Arabidopsis_thaliana_TAIR10-1str-ovlp_transitions.tab
inst/extdata/markov_models/Arabidopsis_thaliana_TAIR10/4nt_genomic_Arabidopsis_thaliana_TAIR10-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Bacillus_subtilis_168_uid57675/1nt_genomic_Bacillus_subtilis_168_uid57675-1str-ovlp.freq.gz
inst/extdata/markov_models/Bacillus_subtilis_168_uid57675/1nt_genomic_Bacillus_subtilis_168_uid57675-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Bacillus_subtilis_168_uid57675/2nt_genomic_Bacillus_subtilis_168_uid57675-1str-ovlp.freq.gz
inst/extdata/markov_models/Bacillus_subtilis_168_uid57675/2nt_genomic_Bacillus_subtilis_168_uid57675-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Bacillus_subtilis_168_uid57675/3nt_genomic_Bacillus_subtilis_168_uid57675-1str-ovlp.freq.gz
inst/extdata/markov_models/Bacillus_subtilis_168_uid57675/3nt_genomic_Bacillus_subtilis_168_uid57675-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Bacillus_subtilis_168_uid57675/4nt_genomic_Bacillus_subtilis_168_uid57675-1str-ovlp.freq.gz
inst/extdata/markov_models/Bacillus_subtilis_168_uid57675/4nt_genomic_Bacillus_subtilis_168_uid57675-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Drosophila_melanogaster_BDGP6/1nt_genomic_Drosophila_melanogaster_BDGP6-1str-ovlp.freq.gz
inst/extdata/markov_models/Drosophila_melanogaster_BDGP6/1nt_genomic_Drosophila_melanogaster_BDGP6-1str-ovlp_transitions.tab
inst/extdata/markov_models/Drosophila_melanogaster_BDGP6/1nt_genomic_Drosophila_melanogaster_BDGP6-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Drosophila_melanogaster_BDGP6/2nt_genomic_Drosophila_melanogaster_BDGP6-1str-ovlp.freq.gz
inst/extdata/markov_models/Drosophila_melanogaster_BDGP6/2nt_genomic_Drosophila_melanogaster_BDGP6-1str-ovlp_transitions.tab
inst/extdata/markov_models/Drosophila_melanogaster_BDGP6/2nt_genomic_Drosophila_melanogaster_BDGP6-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Drosophila_melanogaster_BDGP6/3nt_genomic_Drosophila_melanogaster_BDGP6-1str-ovlp.freq.gz
inst/extdata/markov_models/Drosophila_melanogaster_BDGP6/3nt_genomic_Drosophila_melanogaster_BDGP6-1str-ovlp_transitions.tab
inst/extdata/markov_models/Drosophila_melanogaster_BDGP6/3nt_genomic_Drosophila_melanogaster_BDGP6-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Drosophila_melanogaster_BDGP6/4nt_genomic_Drosophila_melanogaster_BDGP6-1str-ovlp.freq.gz
inst/extdata/markov_models/Drosophila_melanogaster_BDGP6/4nt_genomic_Drosophila_melanogaster_BDGP6-1str-ovlp_transitions.tab
inst/extdata/markov_models/Drosophila_melanogaster_BDGP6/4nt_genomic_Drosophila_melanogaster_BDGP6-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Escherichia_coli_K12/1nt_genomic_Escherichia_coli_K12-1str-ovlp.freq.gz
inst/extdata/markov_models/Escherichia_coli_K12/1nt_genomic_Escherichia_coli_K12-1str-ovlp_transitions.tab
inst/extdata/markov_models/Escherichia_coli_K12/1nt_genomic_Escherichia_coli_K12-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Escherichia_coli_K12/2nt_genomic_Escherichia_coli_K12-1str-ovlp.freq.gz
inst/extdata/markov_models/Escherichia_coli_K12/2nt_genomic_Escherichia_coli_K12-1str-ovlp_transitions.tab
inst/extdata/markov_models/Escherichia_coli_K12/2nt_genomic_Escherichia_coli_K12-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Escherichia_coli_K12/3nt_genomic_Escherichia_coli_K12-1str-ovlp.freq.gz
inst/extdata/markov_models/Escherichia_coli_K12/3nt_genomic_Escherichia_coli_K12-1str-ovlp_transitions.tab
inst/extdata/markov_models/Escherichia_coli_K12/3nt_genomic_Escherichia_coli_K12-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Escherichia_coli_K12/4nt_genomic_Escherichia_coli_K12-1str-ovlp.freq.gz
inst/extdata/markov_models/Escherichia_coli_K12/4nt_genomic_Escherichia_coli_K12-1str-ovlp_transitions.tab
inst/extdata/markov_models/Escherichia_coli_K12/4nt_genomic_Escherichia_coli_K12-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Homo_sapiens_GRCh37/1nt_genomic_Homo_sapiens_GRCh37-1str-ovlp.freq.gz
inst/extdata/markov_models/Homo_sapiens_GRCh37/1nt_genomic_Homo_sapiens_GRCh37-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Homo_sapiens_GRCh37/2nt_genomic_Homo_sapiens_GRCh37-1str-ovlp.freq.gz
inst/extdata/markov_models/Homo_sapiens_GRCh37/2nt_genomic_Homo_sapiens_GRCh37-1str-ovlp_transitions.tab
inst/extdata/markov_models/Homo_sapiens_GRCh37/2nt_genomic_Homo_sapiens_GRCh37-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Homo_sapiens_GRCh37/3nt_genomic_Homo_sapiens_GRCh37-1str-ovlp.freq.gz
inst/extdata/markov_models/Homo_sapiens_GRCh37/3nt_genomic_Homo_sapiens_GRCh37-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Homo_sapiens_GRCh37/4nt_genomic_Homo_sapiens_GRCh37-1str-ovlp.freq.gz
inst/extdata/markov_models/Homo_sapiens_GRCh37/4nt_genomic_Homo_sapiens_GRCh37-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Homo_sapiens_GRCh38/1nt_genomic_Homo_sapiens_GRCh38-1str-ovlp.freq.gz
inst/extdata/markov_models/Homo_sapiens_GRCh38/1nt_genomic_Homo_sapiens_GRCh38-1str-ovlp_transitions.tab
inst/extdata/markov_models/Homo_sapiens_GRCh38/1nt_genomic_Homo_sapiens_GRCh38-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Homo_sapiens_GRCh38/2nt_genomic_Homo_sapiens_GRCh38-1str-ovlp.freq.gz
inst/extdata/markov_models/Homo_sapiens_GRCh38/2nt_genomic_Homo_sapiens_GRCh38-1str-ovlp_transitions.tab
inst/extdata/markov_models/Homo_sapiens_GRCh38/2nt_genomic_Homo_sapiens_GRCh38-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Homo_sapiens_GRCh38/3nt_genomic_Homo_sapiens_GRCh38-1str-ovlp.freq.gz
inst/extdata/markov_models/Homo_sapiens_GRCh38/3nt_genomic_Homo_sapiens_GRCh38-1str-ovlp_transitions.tab
inst/extdata/markov_models/Homo_sapiens_GRCh38/3nt_genomic_Homo_sapiens_GRCh38-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Homo_sapiens_GRCh38/4nt_genomic_Homo_sapiens_GRCh38-1str-ovlp.freq.gz
inst/extdata/markov_models/Homo_sapiens_GRCh38/4nt_genomic_Homo_sapiens_GRCh38-1str-ovlp_transitions.tab
inst/extdata/markov_models/Homo_sapiens_GRCh38/4nt_genomic_Homo_sapiens_GRCh38-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Mycoplasma_genitalium_G37_uid57707/1nt_genomic_Mycoplasma_genitalium_G37_uid57707-1str-ovlp.freq.gz
inst/extdata/markov_models/Mycoplasma_genitalium_G37_uid57707/1nt_genomic_Mycoplasma_genitalium_G37_uid57707-1str-ovlp_transitions.tab
inst/extdata/markov_models/Mycoplasma_genitalium_G37_uid57707/1nt_genomic_Mycoplasma_genitalium_G37_uid57707-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Mycoplasma_genitalium_G37_uid57707/2nt_genomic_Mycoplasma_genitalium_G37_uid57707-1str-ovlp.freq.gz
inst/extdata/markov_models/Mycoplasma_genitalium_G37_uid57707/2nt_genomic_Mycoplasma_genitalium_G37_uid57707-1str-ovlp_transitions.tab
inst/extdata/markov_models/Mycoplasma_genitalium_G37_uid57707/2nt_genomic_Mycoplasma_genitalium_G37_uid57707-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Mycoplasma_genitalium_G37_uid57707/3nt_genomic_Mycoplasma_genitalium_G37_uid57707-1str-ovlp.freq.gz
inst/extdata/markov_models/Mycoplasma_genitalium_G37_uid57707/3nt_genomic_Mycoplasma_genitalium_G37_uid57707-1str-ovlp_transitions.tab
inst/extdata/markov_models/Mycoplasma_genitalium_G37_uid57707/3nt_genomic_Mycoplasma_genitalium_G37_uid57707-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Mycoplasma_genitalium_G37_uid57707/4nt_genomic_Mycoplasma_genitalium_G37_uid57707-1str-ovlp.freq.gz
inst/extdata/markov_models/Mycoplasma_genitalium_G37_uid57707/4nt_genomic_Mycoplasma_genitalium_G37_uid57707-1str-ovlp_transitions.tab
inst/extdata/markov_models/Mycoplasma_genitalium_G37_uid57707/4nt_genomic_Mycoplasma_genitalium_G37_uid57707-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Saccharomyces_cerevisiae/1nt_genomic_Saccharomyces_cerevisiae-1str-ovlp.freq.gz
inst/extdata/markov_models/Saccharomyces_cerevisiae/1nt_genomic_Saccharomyces_cerevisiae-1str-ovlp_transitions.tab
inst/extdata/markov_models/Saccharomyces_cerevisiae/1nt_genomic_Saccharomyces_cerevisiae-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Saccharomyces_cerevisiae/2nt_genomic_Saccharomyces_cerevisiae-1str-ovlp.freq.gz
inst/extdata/markov_models/Saccharomyces_cerevisiae/2nt_genomic_Saccharomyces_cerevisiae-1str-ovlp_transitions.tab
inst/extdata/markov_models/Saccharomyces_cerevisiae/2nt_genomic_Saccharomyces_cerevisiae-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Saccharomyces_cerevisiae/3nt_genomic_Saccharomyces_cerevisiae-1str-ovlp.freq.gz
inst/extdata/markov_models/Saccharomyces_cerevisiae/3nt_genomic_Saccharomyces_cerevisiae-1str-ovlp_transitions.tab
inst/extdata/markov_models/Saccharomyces_cerevisiae/3nt_genomic_Saccharomyces_cerevisiae-1str-ovlp_transitions.tab.gz
inst/extdata/markov_models/Saccharomyces_cerevisiae/4nt_genomic_Saccharomyces_cerevisiae-1str-ovlp.freq.gz
inst/extdata/markov_models/Saccharomyces_cerevisiae/4nt_genomic_Saccharomyces_cerevisiae-1str-ovlp_transitions.tab
inst/extdata/markov_models/Saccharomyces_cerevisiae/4nt_genomic_Saccharomyces_cerevisiae-1str-ovlp_transitions.tab.gz
inst/extdata/yeast_genome/README.md
inst/extdata/yeast_genome/README.txt
inst/extdata/yeast_genome/rand_genome_cds.tab
inst/extdata/yeast_genome/yeast_3nt_freq_whole_genome.tab
inst/extdata/yeast_genome/yeast_cds_2014.tab
inst/extdata/yeast_genome/yeast_orf_lengths_2001.tab
man/AUCfromROCtable.Rd
man/ROCstatistics.Rd
man/VolcanoPlot.Rd
man/featureColors.Rd
man/heatmap.simple.Rd
man/kmerFrequenciesToMarkov.Rd
man/meanEqualityTests.Rd
man/meanEqualityTests.compareSignifFeatures.Rd
man/meanEqualityTests.compareTwoTests.Rd
man/meanEqualityTests.plotVolcano.Rd
man/mulitpleTestingCorrections.plotCorrectedVsPval.Rd
man/mulitpleTestingCorrections.plotPvalDistrib.Rd
man/mulitpleTestingCorrections.plotSignifFeatures.Rd
man/multipleTestingCorrections.Rd
man/plot.ROC.Rd
man/plotPvalCompa.Rd
man/plotROCframe.Rd
man/randIndexDetailed.Rd
man/rnormPerGroup.Rd
man/rowwisePermGroupBalanced.Rd
man/rowwiseRandomNormal.Rd
man/rowwiseSample.Rd
man/sampleClasses.Rd
man/seqToPSSM.Rd
man/shadeArea.Rd
man/shadeTails.Rd
man/stats4bioinfo.Rd
man/statsPerRow.Rd
man/stderPlot.Rd
man/tTestPerRow.Rd
man/tTestPerRow.bootstrap.Rd
man/tTestPerRow.bootstrap.VolcanoBoxPlot.Rd
man/tTestPerRow.bootstrap.hist.Rd
man/tTestPerRow.plotVolcano.Rd
man/verbose.Rd
man/wilcoxTestPerRow.Rd
stats4bioinfo.Rproj
