Files in baj12/idealImmunoTP
Interactive Differential Expression AnaLysis
.Rbuildignore
.circleci/config.yml
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/genesignatures.R
R/ggplotCounts.R
R/goseqTable.R
R/helpers.R
R/iSEE_plug.R
R/ideal-pkg.R
R/ideal.R
R/plotCoefficients.R
R/plot_ma.R
R/plot_volcano.R
R/res2tbl.R
R/table-enhancers.R
R/zzz.R
README.md
_config.yml
_pkgdown.yml
appveyor.yml
docs/404.html
docs/LICENSE-text.html
docs/articles/AdvImmoTutorial.html
docs/articles/AdvImmoTutorial_files/figure-html/pressure-1.png
docs/articles/advImm/AdvImmoTutorial.html
docs/articles/advImm/figures/DESeq2_workflow_2018.png
docs/articles/advImm/figures/bad_dispersion1.png
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docs/articles/advImm/figures/de_theory.png
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docs/articles/advImm/figures/deseq_mean_vs_variance.png
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docs/articles/ideal-usersguide.html
docs/articles/ideal-usersguide_files/crosstalk-1.0.0/css/crosstalk.css
docs/articles/ideal-usersguide_files/crosstalk-1.0.0/js/crosstalk.js
docs/articles/ideal-usersguide_files/crosstalk-1.0.0/js/crosstalk.js.map
docs/articles/ideal-usersguide_files/crosstalk-1.0.0/js/crosstalk.min.js
docs/articles/ideal-usersguide_files/crosstalk-1.0.0/js/crosstalk.min.js.map
docs/articles/ideal-usersguide_files/datatables-binding-0.10/datatables.js
docs/articles/ideal-usersguide_files/datatables-binding-0.4/datatables.js
docs/articles/ideal-usersguide_files/datatables-binding-0.5/datatables.js
docs/articles/ideal-usersguide_files/datatables-binding-0.8/datatables.js
docs/articles/ideal-usersguide_files/datatables-binding-0.9/datatables.js
docs/articles/ideal-usersguide_files/datatables-css-0.0.0/datatables-crosstalk.css
docs/articles/ideal-usersguide_files/dt-core-1.10.16/css/jquery.dataTables.extra.css
docs/articles/ideal-usersguide_files/dt-core-1.10.16/css/jquery.dataTables.min.css
docs/articles/ideal-usersguide_files/dt-core-1.10.16/js/jquery.dataTables.min.js
docs/articles/ideal-usersguide_files/dt-core-1.10.19/css/jquery.dataTables.extra.css
docs/articles/ideal-usersguide_files/dt-core-1.10.19/css/jquery.dataTables.min.css
docs/articles/ideal-usersguide_files/dt-core-1.10.19/js/jquery.dataTables.min.js
docs/articles/ideal-usersguide_files/figure-html/ggpc1-1.png
docs/articles/ideal-usersguide_files/figure-html/ggpc2-1.png
docs/articles/ideal-usersguide_files/figure-html/plotma2-1.png
docs/articles/ideal-usersguide_files/figure-html/plotvolcano2-1.png
docs/articles/ideal-usersguide_files/htmlwidgets-1.2/htmlwidgets.js
docs/articles/ideal-usersguide_files/htmlwidgets-1.3/htmlwidgets.js
docs/articles/ideal-usersguide_files/htmlwidgets-1.5.1/htmlwidgets.js
docs/articles/ideal-usersguide_files/jquery-1.12.4/LICENSE.txt
docs/articles/ideal-usersguide_files/jquery-1.12.4/jquery.min.js
docs/articles/ideal_logo_v2.png
docs/articles/index.html
docs/articles/ss_05_overview.png
docs/articles/ss_08_summaryplots.png
docs/articles/ss_09_genefinder.png
docs/articles/ss_10_funcanalysis.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/deseqresult2DEgenes.html
docs/reference/deseqresult2tbl.html
docs/reference/ggplotCounts-1.png
docs/reference/ggplotCounts.html
docs/reference/goseqTable.html
docs/reference/ideal-pkg.html
docs/reference/ideal.html
docs/reference/index.html
docs/reference/plotCoefficients.html
docs/reference/plot_ma-1.png
docs/reference/plot_ma-2.png
docs/reference/plot_ma.html
docs/reference/plot_volcano-1.png
docs/reference/plot_volcano.html
docs/reference/read_gmt.html
docs/reference/sepguesser.html
docs/reference/sig_heatmap.html
docs/reference/wrapup_for_iSEE.html
inst/CITATION
inst/extdata/DataFlow.Rmd
inst/extdata/about.md
inst/extdata/datainput.md
inst/extdata/design_commas.txt
inst/extdata/design_semicolons.txt
inst/extdata/design_spaces.txt
inst/extdata/design_tabs.txt
inst/extdata/featureCount2input.2022.R
inst/extdata/featureCount2input.R
inst/extdata/help_datasetup.md
inst/extdata/help_funcanalysis.md
inst/extdata/help_genefinder.md
inst/extdata/help_overview.md
inst/extdata/help_plots.md
inst/extdata/help_report.md
inst/extdata/help_results.md
inst/extdata/help_signatureexplorer.md
inst/extdata/help_welcome.md
inst/extdata/ideal_logo_v2.png
inst/extdata/instructions.md
inst/extdata/intro_countsoverview.txt
inst/extdata/intro_datasetup.txt
inst/extdata/intro_firsttour.txt
inst/extdata/intro_funcanalysis.txt
inst/extdata/intro_genefinder.txt
inst/extdata/intro_plots.txt
inst/extdata/intro_report.txt
inst/extdata/intro_results.txt
inst/extdata/intro_signatureexplorer.txt
inst/extdata/irt.Rmd
inst/extdata/welcome.md
inst/www/ideal_logo_v2.png
man/deseqresult2DEgenes.Rd
man/deseqresult2tbl.Rd
man/ggplotCounts.Rd
man/goseqTable.Rd
man/ideal-pkg.Rd
man/idealImmunoTP.Rd
man/plotCoefficients.Rd
man/plot_ma.Rd
man/plot_volcano.Rd
man/read_gmt.Rd
man/sepguesser.Rd
man/sig_heatmap.Rd
man/wrapup_for_iSEE.Rd
runDevel.R
runTest.R
testData.RData
tests/testthat.R
tests/testthat/test_shiny.R
vignettes/advImm/AdvImmoTutorial.Rmd
vignettes/advImm/AdvImmoTutorial.log
vignettes/advImm/figures/DESeq2_workflow_2018.png
vignettes/advImm/figures/bad_dispersion1.png
vignettes/advImm/figures/bad_dispersion2.png
vignettes/advImm/figures/de_theory.png
vignettes/advImm/figures/deseq2_mean_vs_variance2.png
vignettes/advImm/figures/deseq2_workflow_separate.png
vignettes/advImm/figures/deseq2_workflow_separate_dis.png
vignettes/advImm/figures/deseq2_workflow_separate_fit.png
vignettes/advImm/figures/deseq2_workflow_separate_sf.png
vignettes/advImm/figures/deseq2_workflow_separate_shr.png
vignettes/advImm/figures/deseq_dispersion1.png
vignettes/advImm/figures/deseq_dispersion2.png
vignettes/advImm/figures/deseq_mean_vs_variance.png
vignettes/advImm/figures/deseq_median_of_ratios.png
vignettes/advImm/figures/meta_example.png
vignettes/advImm/figures/meta_example2.png
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vignettes/advImm/references/geneNameErrors.pdf
vignettes/ideal-usersguide.Rmd
vignettes/ideal_logo_v2.png
vignettes/ss_05_overview.png
vignettes/ss_08_summaryplots.png
vignettes/ss_09_genefinder.png
vignettes/ss_10_funcanalysis.png
