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8. Change log
hsienchao edited this page Nov 2, 2022
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1 revision
- 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
- 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
- Added case level RNAseq analysis
- RNAseq survival p-value pre-calculation for all coding genes
- Added Xeno type to JSON
- Added junction and TDF track in IGV
- Added data integrity report
- Added multiple high confident setting
- Added germline QCI report
- Added QCI project level summary
- Removed redundant samples in TCGA and ICGA
- Renamed the TCGA count to cBioportal count.
- Updated the GENIE count
- Added Cosmic census gene link
- 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
- Added canonical ENSEMBL track to IGV
- Updated IGV.js to v2.10
- Changed the annotation track in IGV to Gencode v38
- Added CNV summary and download in project page
- Added Cosmic mutational signature v3.
- Added reconCNV for visualization of Sequenza and CNVkit results
- Upgraded igv.js to 1.0.4.
- Added IGV to fusion data. The soft-clipping is on by default.
- Added QCI filtering
- Added download button for CNVkit page
- Fixed links in mutalyzer and CIViC
- Added Labmatrix search
- Added new columns to RNAseqQC
If you have any questions with OncoGenomics DB, please contact us: NCI Oncogenomics: oncogenomics@mail.nih.gov