OncoCNV v7.0

OncoCNV v7.0

OncoCNV v6.9 - more bugs fixed

Fix rare clustering error

OncoCNV v6.8

Better support for "chr" in fasta files and BAM

OncoCNV v6.7

Should not throw an error during the t.test when there are NA data; Ln. 1240 of processSamples.R

ONCOCNV v6.6

processSamples.v2.1.R - version where gene-based p-values are taken into account
processSamples.v2.2.R - version where gene-based p-values are taken into account only if a segmentation breakpoint falls within the gene
processSamples.v2.3.R - version with T-test to get higher p-values
processSamples.v5.0.R,processControl.v5.0.R - version with GC-correction, amplicon-based counts and amplicon length correction
processControl.v5.2.R - uses RCA and Loess instead of ICA and cubic splines
processControl.v5.3.R - sghseg added as an option for profile segmentation, some bugs fixed
processControl.v5.4.R - possiblity to choose number of PCs in PCA is added. Less than 3 PCs for less than 4 controls
processControl.v5.5.R - can treat samples without chrX/Y and "bad" amplicons with zero read counts (bug fixed)
processSamples.v5.6.R - serious bug fixed: losses and gains can be inverted in the previous versions; normalization of profiles with big amplification is improved
processControl.v5.7.R - can process control files with just one sample, in this case it says that PC1=normalized read counts for the control sample
ONCOCNV_getCounts.v5.9.pl - bug with GOTO is solved
processSamples.v6.0.R - "t.test for two identical values" bug solved
processSamples.v6.1.R - does not create an error when no information is available for no amplicons of a given gene
processControl.v6.1.R - does not create NA for the smallest amplicon length if there are more than 5% of such amplicons (change this parameters in the file if needed)
processControl.v6.2.R - bug in v6.1 is corrected - for the smallest aplicon length
ONCOCNV_getCounts.v6.2.pl - does not look for overlaps of regions when there are more than 50000 targeted regions. Otherwise, it takes ages if one does not call bedtools or use Set::IntSpan..
ONCOCNV_getCounts.v6.3.pl - can read .BAM files where there is no "chr" prefix in from of each chromosome name
processSamples.v6.4.R - fixed a bug when there are a few aplicons with an extremely low variance in control; and no variance at all in tumors
processSamples.v6.5.R - can now find losses with 0 reads in several amplicons in a row; can output copy number for chrY and chrM.
processSamples.v6.6.R - does not throw an error when there are large regions with zero reads in the control (this can happen only when there are serious experemental problems).
processControl.v6.6.R - can now process exome-seq data with a file with prob locations (preferably. Otherwise use exons). - Will still take several hours.