hnscc

HNSCC survival analysis, dataset: TCGA HNSCC (head and neck squamous cell carcinoma) function: cutoff finder to deal with the optimized KM P-value

http://35.x.x.x

https://git2go.com/blog/2016/03/30/Git-for-writing-scientific-papers-and-theses.html

https://github.com/texchi2/rticles

https://github.com/ismayc/reedtemplates

Name		Name	Last commit message	Last commit date
Latest commit History 192 Commits
.github/ISSUE_TEMPLATE		.github/ISSUE_TEMPLATE
Manuscript		Manuscript
marginFree		marginFree
marginPlus		marginPlus
marginS		marginS
*.bak		*.bak
.gitignore		.gitignore
Budczies2012_Text_S1.R		Budczies2012_Text_S1.R
DAVID_hnsccBackgroundGenes.txt		DAVID_hnsccBackgroundGenes.txt
DAVID_hnsccForegroundGenes.txt		DAVID_hnsccForegroundGenes.txt
FDR_GDC.R		FDR_GDC.R
GDCRNATools.workflow.R		GDCRNATools.workflow.R
HNSCC.clinical.Fire.Rda		HNSCC.clinical.Fire.Rda
HNSCC.clinical.RNAseq_tobacco.Fire.Rda		HNSCC.clinical.RNAseq_tobacco.Fire.Rda
HNSCC_OS_marginPlus_pvalueBonferroni_pvalueplot.tiff		HNSCC_OS_marginPlus_pvalueBonferroni_pvalueplot.tiff
HNSCC_OS_marginSFP_pvalueBonferroni_KM_candidate_cox.Rda		HNSCC_OS_marginSFP_pvalueBonferroni_KM_candidate_cox.Rda
HNSCC_OS_marginS_THREE_pvalue005_noCancerGene.Rda		HNSCC_OS_marginS_THREE_pvalue005_noCancerGene.Rda
HNSCC_OS_marginS_candidates_Bonferroni.xlsx		HNSCC_OS_marginS_candidates_Bonferroni.xlsx
HNSCC_OS_marginS_candidates_Bonferroni_Table3.xlsx		HNSCC_OS_marginS_candidates_Bonferroni_Table3.xlsx
HNSCC_OS_marginS_candidates_Venn.xlsx		HNSCC_OS_marginS_candidates_Venn.xlsx
HNSCC_OS_marginS_pvalue005_pvalueplot.tiff		HNSCC_OS_marginS_pvalue005_pvalueplot.tiff
HNSCC_OS_marginS_pvalueBonferroni_pvalueplot.tiff		HNSCC_OS_marginS_pvalueBonferroni_pvalueplot.tiff
HNSCC_OS_marginS_pvalue_sorted_noNA_p_adjustS.Rda		HNSCC_OS_marginS_pvalue_sorted_noNA_p_adjustS.Rda
HNSCC_genes_embase5_barplot.tiff		HNSCC_genes_embase5_barplot.tiff
HNSCC_survivalAnalysis_marginS_EVPLL.Rda		HNSCC_survivalAnalysis_marginS_EVPLL.Rda
HNSCC_survivalAnalysis_marginS_FCGBP.Rda		HNSCC_survivalAnalysis_marginS_FCGBP.Rda
HNSCC_survivalAnalysis_marginS_IL19.Rda		HNSCC_survivalAnalysis_marginS_IL19.Rda
HNSCC_survivalAnalysis_marginS_KIAA1683.Rda		HNSCC_survivalAnalysis_marginS_KIAA1683.Rda
HNSCC_survivalAnalysis_marginS_LOC148709.Rda		HNSCC_survivalAnalysis_marginS_LOC148709.Rda
HNSCC_survivalAnalysis_marginS_MYO1H.Rda		HNSCC_survivalAnalysis_marginS_MYO1H.Rda
HNSCC_survivalAnalysis_marginS_NPB.Rda		HNSCC_survivalAnalysis_marginS_NPB.Rda
HNSCC_survivalAnalysis_marginS_PNMA5.Rda		HNSCC_survivalAnalysis_marginS_PNMA5.Rda
HNSCC_survivalAnalysis_marginS_ZNF266.Rda		HNSCC_survivalAnalysis_marginS_ZNF266.Rda
HNSCC_survivalAnalysis_marginS_ZNF557.Rda		HNSCC_survivalAnalysis_marginS_ZNF557.Rda
HNSCC_survivalAnalysis_tobacco_grouping.Rda		HNSCC_survivalAnalysis_tobacco_grouping.Rda
KMplot_OS_tobacco_exposure.png		KMplot_OS_tobacco_exposure.png
KMplot_OS_tobacco_exposure.tiff		KMplot_OS_tobacco_exposure.tiff
Nicotinic_acetylcholone_receptor_signaling_pathway.png		Nicotinic_acetylcholone_receptor_signaling_pathway.png
PANTHER+Pathways_nicotine62genes.txt		PANTHER+Pathways_nicotine62genes.txt
PvalueplotKM.tiff		PvalueplotKM.tiff
PvalueplotKM_10genes.png		PvalueplotKM_10genes.png
PvalueplotKM_10genes.tiff		PvalueplotKM_10genes.tiff
PvalueplotKM_20genes_Bonf.pdf		PvalueplotKM_20genes_Bonf.pdf
PvalueplotKM_9genes.tiff		PvalueplotKM_9genes.tiff
README.html		README.html
README.md		README.md
Rplot.tiff		Rplot.tiff
Rplot01.tiff		Rplot01.tiff
Rplot02.tiff		Rplot02.tiff
Rplot03.tiff		Rplot03.tiff
Rplot04.tiff		Rplot04.tiff
Rplot05.tiff		Rplot05.tiff
Rplot06.tiff		Rplot06.tiff
Rplot07.tiff		Rplot07.tiff
Rplot07_cox_multiHR.tiff		Rplot07_cox_multiHR.tiff
Rplot07_cox_uniHR.png		Rplot07_cox_uniHR.png
Rplot07_cox_uniHR.tiff		Rplot07_cox_uniHR.tiff
Rplot08.pdf		Rplot08.pdf
Rplot08_KMPvalue_multi_HR2p0.tiff		Rplot08_KMPvalue_multi_HR2p0.tiff
Rplot08_KMPvalue_uni_HR2p0.tiff		Rplot08_KMPvalue_uni_HR2p0.tiff
Rplot09_venn_HR0.5.png		Rplot09_venn_HR0.5.png
Rplot09_venn_HR0.5.tiff		Rplot09_venn_HR0.5.tiff
Rplot09_venn_HR1.5.png		Rplot09_venn_HR1.5.png
Rplot09_venn_HR1.5.tiff		Rplot09_venn_HR1.5.tiff
Rplot10.tiff		Rplot10.tiff
Rplot10_Freq_Pvalue.tiff		Rplot10_Freq_Pvalue.tiff
Rplot10_Zscore_Pvalue.png		Rplot10_Zscore_Pvalue.png
Rplot10_Zscore_Pvalue.tiff		Rplot10_Zscore_Pvalue.tiff
Rplot10_Zscore_Pvalue_boxplot.tiff		Rplot10_Zscore_Pvalue_boxplot.tiff
Rplot11.tiff		Rplot11.tiff
Rplot11_venn_hnscc_nicotine.tiff		Rplot11_venn_hnscc_nicotine.tiff
TCGA_HNSCC_marginSFP.R		TCGA_HNSCC_marginSFP.R
TCGA_HNSC_Optimal_Overall_allPlot_unKM_P_multiHR-Figure3.pdf		TCGA_HNSC_Optimal_Overall_allPlot_unKM_P_multiHR-Figure3.pdf
TCPA_proteins237.Rda		TCPA_proteins237.Rda
ZSWIM2_2_pie9416.tiff		ZSWIM2_2_pie9416.tiff
ZSWIM2_archive.Rda		ZSWIM2_archive.Rda
Zscore_Pvalue_scatter.png		Zscore_Pvalue_scatter.png
analysis_export.R		analysis_export.R
cox_multi_Bonf_KMPvalue.png		cox_multi_Bonf_KMPvalue.png
cox_multi_Bonf_KMPvalue.tiff		cox_multi_Bonf_KMPvalue.tiff
cox_multi_FDR_KMPvalue.tiff		cox_multi_FDR_KMPvalue.tiff
cox_multi_uncorrected_KMPvalue.tiff		cox_multi_uncorrected_KMPvalue.tiff
cutofFinder_func_HNSCC.R		cutofFinder_func_HNSCC.R
gmailr_pvalue.csv		gmailr_pvalue.csv
hnscc_DAVID_FuncAnnotChart.tsv		hnscc_DAVID_FuncAnnotChart.tsv
hnscc_DAVID_FuncAnnotClust.tsv		hnscc_DAVID_FuncAnnotClust.tsv
hnscc_github.Rproj		hnscc_github.Rproj
journal.pone.0051862.s001.R		journal.pone.0051862.s001.R
main_marginSFP_HNSCC.R		main_marginSFP_HNSCC.R
marginS_candidate_bad_unimulti_HR2p5.Rda		marginS_candidate_bad_unimulti_HR2p5.Rda
marginS_candidate_good_unimulti_HR0p5.Rda		marginS_candidate_good_unimulti_HR0p5.Rda
pantherChart.txt		pantherChart.txt
pantherChart_TFs_protein.tiff		pantherChart_TFs_protein.tiff
pantherChart_TFs_protein_sub.tiff		pantherChart_TFs_protein_sub.tiff
pantherChart_biological.tiff		pantherChart_biological.tiff
pantherChart_molecularFunc.tiff		pantherChart_molecularFunc.tiff
pantherChart_pathway.tiff		pantherChart_pathway.tiff
panther_14GeneList_inPathways.txt		panther_14GeneList_inPathways.txt
pathwayCommon_RBBP4_hnscc.png		pathwayCommon_RBBP4_hnscc.png
pubmed_articles_5.tiff		pubmed_articles_5.tiff

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