8. Change log - CCRGeneticsBranch/oncogenomics GitHub Wiki
August 18, 2022
Added "rank" column in case expression tab
Added "project group" column to projects
Added new roles "project group manager" and "project group user" who can manage or access whole project group
August 11, 2022
Added "Samples" tab to project page
Added "Cases" tab to project page
Updated project level genotyping page
Expression tab in case page will be shown as matrix format if multiple samples are found in the case
Performance improvement in case page's expression tab
May 13, 2022
Added case level RNAseq analysis
April 26, 2022
RNAseq survival p-value pre-calculation for all coding genes
Added Xeno type to JSON
April 14, 2022
Added junction and TDF track in IGV
Added data integrity report
March 4, 2022
Added multiple high confident setting
Added germline QCI report
Added QCI project level summary
February 4, 2022
Removed redundant samples in TCGA and ICGA
Renamed the TCGA count to cBioportal count.
Updated the GENIE count
Added Cosmic census gene link
January 20, 2022
Updated fusion feature
Removed the code from web site. I’ve made independent python scripts which can convert the pipeline fusion output to the processed format. (See https://github.com/CCRGeneticsBranch/fusionTools)
Use Gencode/ENSEMBL annotation only. Currently annotation: Gencode V37.
Included intronic sequences when the breakpoints are close to the splice sites. The current cutoff is 100bp.
All pipeline fusion results are reported. No filtering applied.
Included RSEM isoform expression if the RSEM files are provided.
No fusion protein will be predicted if the breakpoints are not in CDS.
The default fusion are determined by canonical transcripts.
Exon numbers are provided.
If the breakpoints are not at splice junctions, the sequences between splice sites and breakpoints are provided. This is useful for checking ambiguous breakpoints.
New tiering system.
QCI annotation are included if found.
Spanning read count UI is changed.
Breakpoint regions are provided (CDS, UTR, intron…)
Icons for Sanger fusion/cancer genes.
Pfam domains are updated to latest version.
Added patient level genotyping
Added TCellExTRECT if exome results are found
Tab UI has been changed to bootstrap style
Added diagnosis list in project page if more than 10
November 3, 2021
Added canonical ENSEMBL track to IGV
October 15, 2021
Updated IGV.js to v2.10
Changed the annotation track in IGV to Gencode v38
Added CNV summary and download in project page
October 5, 2021
Added Cosmic mutational signature v3.
August 10, 2021
Added reconCNV for visualization of Sequenza and CNVkit results