Name | Modified | Size | Downloads / Week |
---|---|---|---|
Software | 2013-10-24 | ||
Source | 2013-04-11 | ||
Test Files | 2012-10-16 | ||
readme.txt | 2013-10-25 | 2.4 kB | |
Totals: 4 Items | 2.4 kB | 1 |
===================IMPORTANT INFORMATION===================== FishingCNV comes in two different releases: - GUI version (FishingCNV_X.X.X.zip) - Commandline version (FishingCNV_X.X_Pipeline.tar) =======Recent release notes for commandline version ========= fishingCNV_2.1_pipeline (2013-10-24): - Significant improvement in performance - Simplified output, all chromosome plots combined into one file - RPKM files halved in size, no more duplicates - Added new plots to PDF output - The Rsript now takes flag parameters for: * Minimum segmentation size (between 2-5) * Whether PCA is to be performed * If PCA, number of PCs to remove (default 2) * Whether to double data for single exon CNV detection - Whole exome analyzed at once, no splitting and no generation of temporary files - Improved error handling fishingCNV_2.0_pipeline (2013-10-18): - Significant improvement to the file manipulation code * Java program now takes clearly defined flags * Improved user interface * Improved error handling and logging * Combined all relevant file manipulation code - Rscript improvement for speed and usability - Decoupled file manipulateion code (Java) from statistical analysis (Rscript) to reduce linking errors * Now you call them separately =======Recent release notes for GUI version ================= **Note: major improvements pending, to implement new code from commandline version. FishingCNV_1.5.2 (2013-07-10): - Fixed some rounding errors -- some integer divisions were changed to floating point divisions FishingCNV_1.5.2: - Multiple file selections are now supported in the Browse function FishingCNV_1.5.1: - Added a new feature under the RPKM tab to convert "coverage.sample_interval_summary" files to RPKM - A bug is fixed to allow for different annotations of chromosomes in .bed files * now it accepts both "1" and "chr1" FishingCNV_1.5: - Major updates to the program: * GATK is bundled into the program so that RPKM files can be generated directly from BAM files * Fixed a data-dependent bug in the PCA analysis. Now it will catch all the errors and proceed accordingly. FishingCNV_1.3: - PCA plots are now included in the output