metamaden/recountmethylationManuscriptSupplement
Supplement for the manuscript "Human methylome variation across Infinium 450K data on the Gene Expression Omnibus"

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metamaden/recountmethylationManuscriptSupplement: Supplement for the manuscript "Human methylome variation across Infinium 450K data on the Gene Expression Omnibus"
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Files in metamaden/recountmethylationManuscriptSupplement
Supplement for the manuscript "Human methylome variation across Infinium 450K data on the Gene Expression Omnibus"

.Rbuildignore
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DESCRIPTION
NAMESPACE
R/beadarray_cgctrlmetrics.R R/regex_helpers.R R/utilities.R README.md
inst/.DS_Store
inst/docfiles/main_figures.html
inst/docfiles/supplemental_figures.html
inst/docfiles/supplemental_information.html
inst/docfiles/supplemental_information.pdf
inst/extdata/.DS_Store
inst/extdata/geodata/gseidatyrdat
inst/extdata/geodata/gseyeardata
inst/extdata/geodata/gsmidatyrdat
inst/extdata/geodata/gsmyeardata
inst/extdata/metadata/1548876778.rsheet
inst/extdata/metadata/ccformat.txt
inst/extdata/metadata/ccformat.txt.zip
inst/extdata/metadata/geo_gse-atables_list.rda
inst/extdata/metadata/gsequery_filt.1552256509
inst/extdata/metadata/gsm_jsontitledf.rda
inst/extdata/metadata/md_postprocess.csv
inst/extdata/metadata/md_postprocess.rda
inst/extdata/metadata/md_preprocess.csv
inst/extdata/metadata/md_preprocess.rda
inst/extdata/metadata/mdmap-gsm_35k.rda
inst/extdata/metadata/mdmod.rda
inst/extdata/metadata/obolabels.table.zip
inst/extdata/metadata/old/md-postprocess.csv
inst/extdata/metadata/old/md-postprocess.rda
inst/extdata/metadata/old/md-preprocess.rda
inst/extdata/metadata/old/md_preprocess.csv
inst/extdata/metadata/old/md_preprocess.rda
inst/extdata/metadata/old/metadata_preprocessing.csv
inst/extdata/metadata/old/metadata_preprocessing.rda
inst/extdata/metadata/old/prepmd.rda
inst/extdata/metadata/prepmd.rda
inst/extdata/nct7/.DS_Store
inst/extdata/nct7/.Rhistory
inst/extdata/nct7/anova-filt_nct.table
inst/extdata/nct7/cgids_highvar_nct7.rda
inst/extdata/nct7/cgids_lowvar-lowmean_nct7.rda
inst/extdata/nct7/gsmid-nct7.csv
inst/extdata/nct7/gsmid-nct7.rda
inst/extdata/nct7/lmvp_bin-abs-unique-lowvar_7nct.rda
inst/extdata/nct7/ltxfilt-dnamsummary_highvar_nct7.rda
inst/extdata/pcadata/m-var_blood-vs-leukemia.rda
inst/extdata/pcadata/m-var_brain-vs-braintumor.rda
inst/extdata/pcadata/metadata_pca-labels.rda
inst/extdata/pcadata/pcadat_all-noblood.rda
inst/extdata/pcadata/pcadat_allsamples.rda
inst/extdata/pcadata/pcadat_nct6-nosperm.rda
inst/extdata/pcadata/pcadat_nct7.rda
inst/extdata/tables/table-s1_mdpost_all-gsm-md.csv
inst/extdata/tables/table-s2_qcmd-allgsm.csv
inst/extdata/tables/table-s3_bametrics.csv
inst/extdata/tables/table-s4_storageprep_gseinfo.csv
inst/extdata/tables/table-s5_qcfreq_gsewise.csv
inst/extdata/tables/table-s6_dfgse_nct.csv
inst/extdata/tables/table-s7_pantissue-hypovar_7nct.csv
inst/extdata/tables/table-s8_14k-highvar_7nct.csv
inst/python/dnamhash.py
inst/python/eqplot.py
inst/scripts/.DS_Store
inst/scripts/.Rhistory
inst/scripts/analyses/analyze_highvar_nct7.R inst/scripts/analyses/analyze_lowvar_nct7.R inst/scripts/analyses/anova_filter_nct7.R inst/scripts/analyses/bacontrol_term-enrichment.R inst/scripts/analyses/dnam-var_cancer-normal.R inst/scripts/analyses/get_highvar_nct7.R inst/scripts/analyses/get_lowvar_nct7.R inst/scripts/analyses/pca_analysis_fig3.R inst/scripts/analyses/pca_analysis_fig3a.R inst/scripts/analyses/pca_analysis_fig3b.R inst/scripts/analyses/storagecond_term-enrichment.R inst/scripts/figures/fig1a.R inst/scripts/figures/fig1b.R inst/scripts/figures/fig2a.R inst/scripts/figures/fig2b.R inst/scripts/figures/fig2c.R inst/scripts/figures/fig2d.R inst/scripts/figures/fig3a.R inst/scripts/figures/fig3b.R inst/scripts/figures/fig3c.R inst/scripts/figures/fig3d.R inst/scripts/figures/fig4ab.R inst/scripts/figures/fig4c.R inst/scripts/figures/figS1.R inst/scripts/figures/figS2.R inst/scripts/figures/figS3.R inst/scripts/figures/figS4.R inst/scripts/figures/figS5.R inst/scripts/figures/figS6ac.R inst/scripts/figures/figS6bd.R inst/scripts/figures/figS7.R inst/scripts/figures/figS8.R inst/scripts/metadata/get_gsm_titles.R inst/scripts/metadata/get_msrap_mdmap.R inst/scripts/metadata/jsonfilt.R inst/scripts/metadata/make_gse_annolist.R inst/scripts/metadata/make_md_final.R inst/scripts/metadata/metadata_model_predictions.R inst/scripts/metadata/metadata_postprocessing.R inst/scripts/metadata/metadata_preprocessing.R inst/scripts/metadata/metadata_workflow.R inst/scripts/metadata/soft2json.R inst/scripts/tables/table1.R inst/scripts/tables/tableS1.R inst/scripts/tables/tableS2.R inst/scripts/tables/tableS5.R inst/scripts/tables/tableS7.R inst/scripts/tables/tableS8.R man/appendvar.Rd man/bactrl.Rd man/bathresh.Rd man/get_filt.Rd man/get_pstr.Rd man/get_pstr_neg.Rd man/getblocks.Rd man/match1to2.Rd
vignettes/.DS_Store
vignettes/.Rhistory
vignettes/main_figures.Rmd
vignettes/rm_refs.bib
vignettes/supplemental_figures.Rmd vignettes/supplemental_information.Rmd
metamaden/recountmethylationManuscriptSupplement documentation built on May 31, 2021, 5:27 a.m.

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