Recent changes to Instructions

Instructions modified by Keith Ching

Keith Ching — Tue, 13 Feb 2018 16:38:33 -0000

--- v53
+++ v54
@@ -45,3 +45,4 @@
 [methyl_mut]
 [meta_fisher] : Fisher test of two meta categorical fields.
 [snp] : Test SNPs vs. expression levels
+[slide_tab]: Show associated slide images

Instructions modified by Keith Ching

Keith Ching — Wed, 31 Jan 2018 00:17:19 -0000

--- v52
+++ v53
@@ -38,6 +38,7 @@
 [meta_heatmap]
 [meta_search]
 [matrix] : Output expression, CNV, and mutations in table format.
+[gene_loci]
 [tabledump]
 [venn] : Create venn diagrams based on molecular features.
 [combinations] : Find genes correlated or enriched between groups defined by combination scores.

Instructions modified by Keith Ching

Keith Ching — Wed, 31 Jan 2018 00:12:13 -0000

--- v51
+++ v52
@@ -33,6 +33,7 @@
 [sample_report] : List cnv and mutations present for a given sample.
 [sample_search] : Search for sample names in the database.
 [marker_report] : Count samples that meet the criteria for positive or negative sets of putative biomarkers.
+[mirna_barplot]
 [survival] : Plot survival plots (TCGA only)
 [meta_heatmap]
 [meta_search]

Instructions modified by Keith Ching

Keith Ching — Mon, 25 Sep 2017 23:31:19 -0000

--- v50
+++ v51
@@ -42,3 +42,4 @@
 [combinations] : Find genes correlated or enriched between groups defined by combination scores.
 [methyl_mut]
 [meta_fisher] : Fisher test of two meta categorical fields.
+[snp] : Test SNPs vs. expression levels

Instructions modified by Keith Ching

Keith Ching — Sat, 24 Jun 2017 15:46:01 -0000

--- v49
+++ v50
@@ -41,4 +41,4 @@
 [venn] : Create venn diagrams based on molecular features.
 [combinations] : Find genes correlated or enriched between groups defined by combination scores.
 [methyl_mut]
-[fisher_mutation_meta]
+[meta_fisher] : Fisher test of two meta categorical fields.

Instructions modified by Keith Ching

Keith Ching — Sat, 24 Jun 2017 15:43:41 -0000

--- v48
+++ v49
@@ -23,6 +23,7 @@
 [pca_plot] : PCA plot whole expression data *dev
 ***Mutation***
 [fisher_mutation]
+[meta_mutation] : Fisher test for mutation status and metadata
 [mutation_exp] : Find genes with mutations that have statistically different expression of the selected gene.
 [mutation_table] : create table of mutations.
 [mutation_report] : Database wide survey of mutations in a gene.

Instructions modified by Keith Ching

Keith Ching — Sat, 24 Jun 2017 15:41:31 -0000

--- v47
+++ v48
@@ -20,6 +20,7 @@
 [expression_meta] : Find genes correlated or enriched between groups defined by meta data.
 [expression_mirna] : Find which genes are statistically different between groups defined by mirna status.
 [expression_exon]
+[pca_plot] : PCA plot whole expression data *dev
 ***Mutation***
 [fisher_mutation]
 [mutation_exp] : Find genes with mutations that have statistically different expression of the selected gene.

Instructions modified by Keith Ching

Keith Ching — Wed, 25 Jan 2017 01:45:18 -0000

--- v46
+++ v47
@@ -38,5 +38,5 @@
 [tabledump]
 [venn] : Create venn diagrams based on molecular features.
 [combinations] : Find genes correlated or enriched between groups defined by combination scores.
-[methylation_mut]
+[methyl_mut]
 [fisher_mutation_meta]

Instructions modified by Keith Ching

Keith Ching — Wed, 25 Jan 2017 01:42:17 -0000

--- v45
+++ v46
@@ -39,3 +39,4 @@
 [venn] : Create venn diagrams based on molecular features.
 [combinations] : Find genes correlated or enriched between groups defined by combination scores.
 [methylation_mut]
+[fisher_mutation_meta]

Instructions modified by Keith Ching

Keith Ching — Wed, 07 Dec 2016 02:23:25 -0000

--- v44
+++ v45
@@ -38,3 +38,4 @@
 [tabledump]
 [venn] : Create venn diagrams based on molecular features.
 [combinations] : Find genes correlated or enriched between groups defined by combination scores.
+[methylation_mut]