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sbabyanusha committed Aug 14, 2023
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## Aug 1, 2023
* **Enhancement**: One-sided Fisher's exact tests were changed to be two-sided. The affected pages are:
* Results View Page - Mutual Exclusivity Tab
* Results View Page - Comparison Tab - Genomic Alterations Tab
* Comparison Page - Genomic Alterations Tab
* Comparison Page - Mutations Tab

Please note that the Mutations tab on the Comparison page is a recent feature and was introduced with the two-sided Fisher's exact test already implemented.

Several users pointed out that using a one-sided test was incorrect for these comparisons. Please see discussions [here](https://github.com/cBioPortal/cbioportal/issues/9943) for more information.

## May 2, 2023
* **New Feature**: The mutations tab now shows variant annotations from the [repository of Variant with Unexpected Effects (reVUE)](https://www.cancerrevue.org/).
<img src="https://user-images.githubusercontent.com/16869603/234271379-6a0876ea-8477-426e-a0e4-5e0b0b66aef9.gif" width="700" />

## Apr 11, 2023
* **New Feature**: Disable autocommit and manually commit filters in study view. Manually commit filters can improve cBioPortal performance when query large dataset.
<img src="https://user-images.githubusercontent.com/3323006/221857599-1eb6e9a5-55c7-4fb5-bc14-283699be0990.png" width="700" />
<img src="https://user-images.githubusercontent.com/3323006/221858244-bf359850-79b5-4f9c-8008-6b5271721854.png" width="700" />

## Apr 5, 2023
## Aug 15, 2023
* **Added data** consisting of 2,472 samples from 5 studies:
* [Lung Adenocarcinoma Met Organotropism (MSK, Cancer Cell 2023)](https://www.cbioportal.org/study/summary?id=luad_mskcc_2023_met_organotropism) *2653 samples*
* [Acute Myeloid Leukemia (OHSU, Cancer Cell 2022)](https://www.cbioportal.org/study/summary?id=aml_ohsu_2022) *942 samples*
* [Colon Cancer (Sidra-LUMC AC-ICAM, Nat Med 2023)](https://www.cbioportal.org/study/summary?id=coad_silu_2022) *348 samples*
* [Pediatric Neuroblastoma (MSK, Nat Genet 2023)](https://www.cbioportal.org/study/summary?id=nbl_msk_2023) *223 samples*
* [Colorectal Adenocarcinoma (MSK, Nat Commun 2022)](https://www.cbioportal.org/study/summary?id=bowel_colitis_msk_2022) *180 samples*
* [Bladder Cancer (Columbia University/MSK, Cell 2018)](https://www.cbioportal.org/study/summary?id=bladder_columbia_msk_2018) *130 samples*
* [Myoepithelial Carcinomas of Soft Tissue (WCM, CSH Molecular Case Studies 2022)](https://www.cbioportal.org/study/summary?id=stmyec_wcm_2022) *12 samples*

* **Gene Tables Update** Updated tables of genes (main and alias), based on [Apr 1, 2023 HGNC release](http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/). See seedDB release note [here](https://github.com/cBioPortal/datahub/tree/master/seedDB#latest-seed-database) for details.

* **Data Improvement**
* Pan-can studies methylation addition: methylation profile 450K is added to all 32 TCGA Pan-Can studies, in generic assay format. Data source: [GDC](https://gdc.cancer.gov/node/977). Example: Search by gene or probe from dropdown, to add a chart in study view, a track in Oncoprint (single study query only), or plots in plots tab.
<img width="1151" alt="Screen Shot 2023-08-14 at 1 57 29 PM" src="https://github.com/cBioPortal/datahub/assets/61431648/80ce4e7f-84c0-4de4-8cec-deaa79236201">

* Pan-can studies Ancestry addition: Genetic Ancestry data is added to all 32 TCGA Pan-Can studies, in generic assay format. Data source: [GDC](https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020). Example: Search by each ancestry from dropdown, to add a chart in study view, a track in Oncoprint.
<img width="1129" alt="Screen Shot 2023-08-14 at 4 26 22 PM" src="https://github.com/cBioPortal/datahub/assets/61431648/1e5a212c-518c-4eb1-add4-330452c28926">

## Mar 29, 2023
* **Added data** consisting of 2,472 samples from 5 studies:
* [Bladder Cancer (MSK, Cell Reports 2022)](https://www.cbioportal.org/study/summary?id=paired_bladder_2022) *1659 samples*
* [Gastrointestinal Stromal Tumor (MSK, NPJ Precis Oncol 2023)](https://www.cbioportal.org/study/summary?id=gist_msk_2022) *499 samples*
Expand All @@ -29,25 +28,6 @@
* **Data Improvement**
* Added TERT promoter mutation status to [Melanomas (TCGA, Cell 2015)](https://www.cbioportal.org/study/summary?id=skcm_tcga_pub_2015), [Papillary Thyroid Carcinoma (TCGA, Cell 2014)](https://www.cbioportal.org/study/summary?id=thca_tcga_pub) TCGA studies.

## Apr 4, 2023
* **New Feature**: Allow numeric data type for custom data charts.
<img src="https://user-images.githubusercontent.com/33220871/222459360-9c251f7f-1005-442f-811d-dd1ee1103161.png" width="700" />
<img src="https://user-images.githubusercontent.com/33220871/222460439-ac7007c8-059a-4ecc-816c-90752adff444.png" width="700" />

This also allows to have numerical custom data after we query based on genes (custom data 2 in the image):
<img src="https://user-images.githubusercontent.com/33220871/223729410-03a094f4-7671-453f-b8b8-f7bc10b61c7c.png" width="700" />
<img src="https://user-images.githubusercontent.com/33220871/223729522-fd9e19e2-6218-40d4-b9fb-f253c4faa858.png" width="700" />

## Jan 10, 2023
* **New Feature**: New Pathways tab on the Group Comparison view.
[Example: Primary vs Metastasis samples in MSK-IMPACT Clinical Sequencing Cohort](https://www.cbioportal.org/comparison/pathways?comparisonId=61791fa92e3200072db9b64e&groupOrder=%5B%22Primary%22%2C%22Metastasis%22%5D)
<img src="https://user-images.githubusercontent.com/15748980/235750129-661682f7-6593-4b7e-8873-ebba70eeae32.png" width="700" />

## Dec 13, 2022
* **New Feature**: New Mutations tab on the Group Comparison view.
[Example: Primary vs Metastasis samples in MSK-IMPACT Clinical Sequencing Cohort](https://www.cbioportal.org/comparison/mutations?comparisonId=61791fa92e3200072db9b64e&groupOrder=%5B%22Primary%22%2C%22Metastasis%22%5D)
<img src="https://user-images.githubusercontent.com/15748980/235748831-78652ccd-b3ab-496f-9626-74ceb8c7230d.png" width="700" />

## Oct 12, 2022
* **Added data** consisting of 1,459 samples from 10 studies:
* [Hepatocellular Carcinoma (MERiC/Basel, Nat Commun. 2022)](https://www.cbioportal.org/study/summary?id=hcc_meric_2021) *122 samples*
Expand All @@ -60,13 +40,6 @@
* [Mixed Tumors: Selpercatinib RET Trial (MSK, Nat Commun. 2022)](https://www.cbioportal.org/study/summary?id=mixed_selpercatinib_2020) *188 samples*
* [Low-Grade Serous Ovarian Cancer (MSK, Clin Cancer Res 2022)](https://www.cbioportal.org/study/summary?id=lgsoc_mapk_msk_2022) *119 samples*
* [Urothelial Carcinoma (BCAN/HCRN 2022)](http://www.cbioportal.org/study/summary?id=blca_bcan_hcrn_2022) *203 samples*

## Sep 6, 2022
* **Enhancement**: Oncoprint can now save clinical tracks after login
<img src="https://user-images.githubusercontent.com/3323006/188828765-ded10947-7343-49dd-b605-50b58b67a388.png" width="700" />

## Aug 11, 2022
* **New Major Release**: **v5.0.0** release drops support for fusions in the mutation data format. Going forward fusions can only be imported in the Structural Variant (SV) format. This is mainly a refactoring effort to simplify the codebase and pave the way for the development of novel structural variant visualizations in the future. For cBioPortal instance maintainer, please reference our [Migration Guide](https://docs.cbioportal.org/migration-guide/#v4---v5) for instruction.

## Jul 26, 2022
* **Added data** consisting of 6,631 samples from 7 studies:
Expand All @@ -78,10 +51,6 @@
* [Pan-cancer Analysis of Advanced and Metastatic Tumors (BCGSC, Nature Cancer 2020)](https://www.cbioportal.org/study/summary?id=pog570_bcgsc_2020) *570 samples*
* [Prostate Adenocarcinoma (MSK, Clin Cancer Res. 2022)](https://www.cbioportal.org/study/summary?id=prad_pik3r1_msk_2021) *1,417 samples*

## May 31, 2022
* **New Feature**: Added Quartiles, Median split and Generate bins options for bar charts on the study view page, where Generate bins allows user to define bin size and min value
<img src="https://user-images.githubusercontent.com/53996876/151772297-f0aa55ef-5bb4-4e26-8f9b-b0a2369fff71.png" width="700" />

## May 12, 2022
* **New Feature**: Show cohort alteration frequencies in pathways from [NDEx](https://www.ndexbio.org/iquery/) on the _Results View_. [Example: Glioblastoma signaling pathways in MSK-IMPACT (2017) cohort](https://bit.ly/3sE4UqD)

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