Recent changes to sample_report

sample_report modified by Keith Ching

Keith Ching — Wed, 25 Nov 2015 01:29:48 -0000

--- v2
+++ v3
@@ -10,3 +10,5 @@
 Mutation table by source.

 TCGA example [query](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=TCGA-GBM&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=3&cnvminbp=10000&source=TCGA-GBM&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&cells=TCGA-06-5414-01A&exp_ic50_high=500&tsvtable=sample_report&METACOLORS=green+blue&venn_segment=none&sort=mean&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&cnvamp=2&venncnvgene1=%3e1&tissues=ALL&expmut_numresults=25&vennexpgene1=%3e10&venncnvgene2=%3e1&vennexpgene4=%3e10&expcore_colors=red+blue+green+violet+orange+yellow+black&venncnvgene5=%3e1&mut_expression_method=t-test&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)
+
+Cell line HCT116 example [query](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=ALL&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=3&cnvminbp=10000&source=CCLE&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&cells=hct116&exp_ic50_high=500&tsvtable=sample_report&METACOLORS=green+blue&venn_segment=none&sort=mean&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&sample_cnvminsnp=10&cnvamp=2&venncnvgene1=%3e1&sample_cnv=0.75&tissues=ALL&vennexpgene1=%3e10&expmut_numresults=25&venncnvgene2=%3e1&vennexpgene4=%3e10&expcore_colors=red+blue+green+violet+orange+yellow+black&venncnvgene5=%3e1&mut_expression_method=t-test&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

sample_report modified by Keith Ching

Keith Ching — Wed, 25 Nov 2015 01:27:28 -0000

--- v1
+++ v2
@@ -8,3 +8,5 @@
 Can adjust the mean and minsnp cutoffs.  Can be used to dump the segmentation table by gene symbol.

 Mutation table by source.
+
+TCGA example [query](http://54.149.52.246/cgi-bin/RPPA/cellx.cgi?expstat_high=10&compound_sourcename=ALL&kcluster=2&exp_ic50_low=100&maxsize=10&expmirna_numresults=25&combo_low=100&PLOTPOS=bottomright&vennexpgene6=%3e10&target=EGFR&ic50low=100&expcnv_colors=red+blue+green+violet+orange+yellow+black&mutation_source=TCGA-GBM&combination_id=ALL&expcore_scale=none&expcnv_numresults=25&expmirna_low=1&activehtab=3&cnvminbp=10000&source=TCGA-GBM&venncnvgene4=%3e1&minsize=100&combination_datatype=ALL&vennexpgene3=%3e10&SUBMIT=SUBMIT&expstat_direction=both&expcor_numresults=25&expmirna_high=1&combo_cnv_cutoff=1&expcore_method=correlation&PLOTCUTOFFAXIS=Z&cells=TCGA-06-5414-01A&exp_ic50_high=500&tsvtable=sample_report&METACOLORS=green+blue&venn_segment=none&sort=mean&combo_high=500&expcnv_low=1&expcore_top=100&expcore_datasets=10&cnvamp=2&venncnvgene1=%3e1&tissues=ALL&expmut_numresults=25&vennexpgene1=%3e10&venncnvgene2=%3e1&vennexpgene4=%3e10&expcore_colors=red+blue+green+violet+orange+yellow+black&venncnvgene5=%3e1&mut_expression_method=t-test&searchtype=co-occur&venncnvgene6=%3e1&vennexpgene7=%3e10&venncnvgene7=%3e1&venncnvgene3=%3e1&expmirna_colors=red+blue+green+violet+orange+yellow+black&cnvdel=-2&vennexpgene2=%3e10&expcore_direction=both&ic50high=500&expcnv_minsize=10&expcnv_high=1&vennexpgene5=%3e10&mean=2&expcnv_maxsize=10&expstat_low=4&percentile=5&expstat_numresults=25&cnvminsnp=10)

sample_report modified by Keith Ching

Keith Ching — Wed, 05 Aug 2015 19:17:24 -0000

Sample report returns a detailed list about a single sample.

TCGA slide viewer link.

Any Meta data stored about that sample.

CNV table of genes exceeding an absolute mean of 0.75
Can adjust the mean and minsnp cutoffs. Can be used to dump the segmentation table by gene symbol.

Mutation table by source.