Recent changes to Version History

Version History modified by Keith Ching

Keith Ching — Tue, 08 Mar 2016 21:47:38 -0000

--- v5
+++ v6
@@ -39,3 +39,12 @@
 Addition of new datasets.
 Modified UI.
 Additional analysis functions.
+
+Development
+
+Import of TCGA-LAML meta data from NEJM publication.
+Multiple gene expression vs. meta data plot.
+
+venn_summary, addition of option to remove from consideration samples without both CNV and mutation data.
+
+fix the summary table for matrix ( was not median centering data before calculation )

Version History modified by Keith Ching

Keith Ching — Wed, 25 Nov 2015 01:12:15 -0000

--- v4
+++ v5
@@ -33,3 +33,9 @@

 Bug fixes:
 Fixed merge CNV bug, excluded first line of the table.
+
+November 2015
+Update TCGA data.
+Addition of new datasets.
+Modified UI.
+Additional analysis functions.

Version History modified by Keith Ching

Keith Ching — Thu, 23 Apr 2015 23:42:00 -0000

--- v3
+++ v4
@@ -29,7 +29,7 @@
 Use mutation count per sample as a "gene" expression value.
 eg. tests for mutation burden vs. cnv, mutation, metadata, expression.

-Search criteria for CNV modified from >= 10 SNPs to >= 5 SNPs.  Minimum length modified from 10kb to 90bp.
+Search criteria for CNV modified from >= 10 SNPs to >= 5 SNPs.  Minimum length modified from 10kb to 90bp. Applies to genome wide CNV tests.  For expression plot, the default is still 10 SNPs, 10kb. Can be configured by changing the values in the minsnp, minbp boxes.

 Bug fixes:
 Fixed merge CNV bug, excluded first line of the table.

Version History modified by Keith Ching

Keith Ching — Tue, 21 Apr 2015 21:18:15 -0000

--- v2
+++ v3
@@ -13,6 +13,7 @@
 GSE4475
 GSE53482
 GSE6338
+Meta data annotations for TCGA from PMID:25765070

 Removed redundant TCGA mutations.

Version History modified by Keith Ching

Keith Ching — Tue, 21 Apr 2015 21:15:49 -0000

--- v1
+++ v2
@@ -22,6 +22,8 @@
 Find mutations with differential expression levels.
 Added pan TCGA dataset option (TCGA-TOTAL)
 Added lm fit option to expression plot.
+Added box plots of expression vs. CNV or mutation status to expression_plot.
+Beta 3D expression plot.

 Use mutation count per sample as a "gene" expression value.
 eg. tests for mutation burden vs. cnv, mutation, metadata, expression.

Version History modified by Keith Ching

Keith Ching — Tue, 21 Apr 2015 21:13:04 -0000

July 2014
Initial import

November 2014
Update TCGA data sets. Release for PSB paper.

April 2015
Update TCGA data sets.

Added Astrazenica cell line collection. (U133P2 gene expression microarrays)
GSE10846
GSE19069
GSE4475
GSE53482
GSE6338

Removed redundant TCGA mutations.

Functionality:
Survival plots based on expression or miRNA levels.
Find CNV with differential expression levels.
Find mutations with differential expression levels.
Added pan TCGA dataset option (TCGA-TOTAL)
Added lm fit option to expression plot.

Use mutation count per sample as a "gene" expression value.
eg. tests for mutation burden vs. cnv, mutation, metadata, expression.

Search criteria for CNV modified from >= 10 SNPs to >= 5 SNPs. Minimum length modified from 10kb to 90bp.

Bug fixes:
Fixed merge CNV bug, excluded first line of the table.