Files in zhezhangsh/DEGandMore
.DS_Store
.Rapp.history
.gitignore
DEGandMore.Rproj
DESCRIPTION
NAMESPACE
R/.DS_Store
R/.Rapp.history
R/CalculateRand.R
R/CombineMean.R
R/CombinePvalue.R
R/CompareProportionGroups.R
R/ConvertMatrixByRank.R
R/CreateClReport.R
R/CreateDdReport.R
R/CreateDeReport.R
R/CreateOiReport.R
R/CrossPlatformDE.R
R/DeAbsSeq.R
R/DeAldex2.R
R/DeBBSeq.R
R/DeBGmix.R
R/DeBader.R
R/DeBallgown.R
R/DeBaySeq.R
R/DeBridge.R
R/DeDeSeq.R
R/DeDeSeq2.R
R/DeDegSeq.R
R/DeDexus.R
R/DeEbSeq.R
R/DeEdgeR.R
R/DeEdgeRun.R
R/DeGPSeq.R
R/DeLMGene.R
R/DeLimma.R
R/DeMetaseqR.R
R/DeNBPSeq.R
R/DeNoiSeq.R
R/DePlgem.R
R/DePoissonSeq.R
R/DeRBM.R
R/DeRNAseq.R
R/DeRNAseq.Rd
R/DeROTS.R
R/DeRankP.R
R/DeSSeq.R
R/DeSam.R
R/DeSamSeq.R
R/DeShrinkBayes.R
R/DeT.R
R/DeTSPM.R
R/DeTweeDeSeq.R
R/DeVoomLimma.R
R/DeWelch.R
R/DeWilcoxon.R
R/DeWrapper.R
R/DeWrapper.Rd
R/DegHeatmap.R
R/DegPCA.R
R/FilterByNN.R
R/GSEAviaJava.r
R/GeneList2Datatable.R
R/GeneList2Html.R
R/GsaWrapper.R
R/GseaKegg.R
R/HelpDe.R
R/IndexDeRes.R
R/NormWrapper.R
R/NormalizeRNAseq.R
R/OptimizeClustering.R
R/OraWrapper.R
R/OutputDe.R
R/PrepareDe.R
R/PrepareGSEA.r
R/SummarizeGSEA.r
R/SummarizePiano.R
R/SummarizeStatCl.R
R/TransformTxMatrix.R
R/WriteExcel.R
README.md
data/.DS_Store
data/.Rapp.history
data/De.RData
data/DeMethodMeta.RData
data/DeMethodMeta_All.RData
data/count_example.rdata
data/group_example.rdata
data/result_example.rdata
examples/.DS_Store
examples/BatchEffect/BatchEffect.Rmd
examples/BatchEffect/BatchEffect.yml
examples/DdReport/Dd3Report.Rmd
examples/DdReport/Dd3Report.yml
examples/DdReport/DdReport.Rmd
examples/DdReport/DdReport.html
examples/DdReport/DdReport.yml
examples/DeReport/DeReport.Rmd
examples/DeReport/DeReport.yml
examples/DeReport/DeReport_old.Rmd
examples/DeReport/DeReport_v1.Rmd
examples/DeReport/default_set_human_5-1000.rds
examples/DeReport/default_set_worm_5-1000.rds
examples/DeReport/inputs.rds
examples/DeReport/output.html
examples/IdentifyOutlier/identify_outlier.Rmd
examples/IdentifyOutlier/identify_outlier.html
examples/IdentifyOutlier/identify_outlier.yml
examples/MultiGroupCluster/ClDetail.Rmd
examples/MultiGroupCluster/ClReport.Rmd
examples/MultiGroupCluster/ClReport.html
examples/MultiGroupCluster/ClReport.yml
examples/MultiGroupCluster/default_set_rat_5-1000.rds
examples/RNAseq_Read_Count/count_example.csv
examples/RNAseq_Read_Count/count_example.html
examples/RNAseq_Read_Count/count_example.rda
examples/RNAseq_Read_Count/count_example.rdata
examples/RNAseq_Read_Count/count_example.rds
examples/RNAseq_Read_Count/count_example.txt
examples/RNAseq_Read_Count/count_example.xls
examples/RNAseq_Read_Count/count_example.xlsx
examples/geneset_collections/default_set_human_5-1000.rds
examples/geneset_collections/default_set_mouse_5-1000.rds
examples/geneset_collections/default_set_rat_5-1000.rds
examples/geneset_collections/default_set_worm_5-1000.rds
examples/gsea/GENE_SYMBOL.chip
examples/gsea/GSEA_example.cls
examples/gsea/GSEA_example.gct
examples/gsea/GSEA_example.r
examples/gsea/GSEA_example.yaml
examples/gsea/c2.cp.kegg.v5.0.symbols.gmt
examples/gsea/c2.cp.reactome.v5.0.symbols.gmt
examples/gsea/gsea2-2.2.0.jar
examples/gsea/h.all.v5.0.symbols.gmt
export_functions.r
html/RNAseq_2G.Rmd
html/RNAseq_2G.html
html/RNAseq_2G_files/bootstrap-3.3.5/css/bootstrap-theme.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/bootstrap-theme.css.map
html/RNAseq_2G_files/bootstrap-3.3.5/css/bootstrap-theme.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/bootstrap.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/bootstrap.css.map
html/RNAseq_2G_files/bootstrap-3.3.5/css/bootstrap.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/cerulean.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/cosmo.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/flatly.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/Lato.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/LatoBold.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/LatoItalic.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/NewsCycle.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/NewsCycleBold.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/OpenSans.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/OpenSansBold.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/OpenSansBoldItalic.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/OpenSansItalic.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/OpenSansLight.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/OpenSansLightItalic.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/Raleway.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/RalewayBold.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/Roboto.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/RobotoBold.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/RobotoLight.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/RobotoMedium.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/SourceSansPro.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/SourceSansProBold.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/SourceSansProItalic.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/SourceSansProLight.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/fonts/Ubuntu.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/css/journal.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/lumen.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/paper.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/readable.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/sandstone.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/simplex.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/spacelab.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/united.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/css/yeti.min.css
html/RNAseq_2G_files/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.eot
html/RNAseq_2G_files/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.svg
html/RNAseq_2G_files/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.ttf
html/RNAseq_2G_files/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff
html/RNAseq_2G_files/bootstrap-3.3.5/fonts/glyphicons-halflings-regular.woff2
html/RNAseq_2G_files/bootstrap-3.3.5/js/bootstrap.js
html/RNAseq_2G_files/bootstrap-3.3.5/js/bootstrap.min.js
html/RNAseq_2G_files/bootstrap-3.3.5/js/npm.js
html/RNAseq_2G_files/bootstrap-3.3.5/shim/html5shiv.min.js
html/RNAseq_2G_files/bootstrap-3.3.5/shim/respond.min.js
html/RNAseq_2G_files/highlight/default.css
html/RNAseq_2G_files/highlight/highlight.js
html/RNAseq_2G_files/highlight/textmate.css
html/RNAseq_2G_files/jquery-1.11.3/jquery.min.js
html/RNAseq_2G_files/jqueryui-1.11.4/README
html/RNAseq_2G_files/jqueryui-1.11.4/images/ui-icons_444444_256x240.png
html/RNAseq_2G_files/jqueryui-1.11.4/images/ui-icons_555555_256x240.png
html/RNAseq_2G_files/jqueryui-1.11.4/images/ui-icons_777620_256x240.png
html/RNAseq_2G_files/jqueryui-1.11.4/images/ui-icons_777777_256x240.png
html/RNAseq_2G_files/jqueryui-1.11.4/images/ui-icons_cc0000_256x240.png
html/RNAseq_2G_files/jqueryui-1.11.4/images/ui-icons_ffffff_256x240.png
html/RNAseq_2G_files/jqueryui-1.11.4/index.html
html/RNAseq_2G_files/jqueryui-1.11.4/jquery-ui.css
html/RNAseq_2G_files/jqueryui-1.11.4/jquery-ui.js
html/RNAseq_2G_files/jqueryui-1.11.4/jquery-ui.min.css
html/RNAseq_2G_files/jqueryui-1.11.4/jquery-ui.min.js
html/RNAseq_2G_files/jqueryui-1.11.4/jquery-ui.structure.css
html/RNAseq_2G_files/jqueryui-1.11.4/jquery-ui.structure.min.css
html/RNAseq_2G_files/jqueryui-1.11.4/jquery-ui.theme.css
html/RNAseq_2G_files/jqueryui-1.11.4/jquery-ui.theme.min.css
html/RNAseq_2G_files/navigation-1.1/FileSaver.min.js
html/RNAseq_2G_files/navigation-1.1/codefolding.js
html/RNAseq_2G_files/navigation-1.1/sourceembed.js
html/RNAseq_2G_files/navigation-1.1/tabsets.js
html/RNAseq_2G_files/tocify-1.9.1/jquery.tocify.css
html/RNAseq_2G_files/tocify-1.9.1/jquery.tocify.js
html/index.html
html/index.md
html/index_alone.html
html/methods.html
html/methods_files/datatables-binding-0.2/datatables.js
html/methods_files/dt-core-1.10.12/css/jquery.dataTables.extra.css
html/methods_files/dt-core-1.10.12/css/jquery.dataTables.min.css
html/methods_files/dt-core-1.10.12/js/jquery.dataTables.min.js
html/methods_files/htmlwidgets-0.7/htmlwidgets.js
html/methods_files/jquery-1.12.4/LICENSE.txt
html/methods_files/jquery-1.12.4/jquery.min.js
html/methods_files/nouislider-7.0.10/jquery.nouislider.min.css
html/methods_files/nouislider-7.0.10/jquery.nouislider.min.js
html/methods_files/selectize-0.12.0/selectize.bootstrap3.css
html/methods_files/selectize-0.12.0/selectize.min.js
installer.r
