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Update news 2023 - Mar 2024 #10691

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Mar 7, 2024
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Update news 2023 - Mar 2024 #10691

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Update news 2023 - Feb 2024
inodb Mar 6, 2024
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Update granular CNA news wording
inodb Mar 6, 2024
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change wording SV tab in news
inodb Mar 6, 2024
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Make Example style in news consistent
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Add 2024 items
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49 changes: 45 additions & 4 deletions docs/News.md
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## Mar 5, 2024
* **Local Installations Feature**: Make representation of custom driver annotation configurable:
![image](https://github.com/cBioPortal/cbioportal/assets/1334004/f67fd82f-1789-4427-9ca1-f17fc70c1a09)

## Feb 7, 2024
* **New feature**: The _Datasets Page_ now lists what studies have samples profiled for Structural Variants:
![image](https://github.com/cBioPortal/cbioportal/assets/1334004/0e4e73e4-d9d8-417d-912c-710163480905)
* **New Major Release**: **v6.0.0** includes a major repackaging of the backend software to improve the development experience. The backend has been upgraded to use Java Spring Boot v3.1.4. The CORE and MAF modules have been moved to new repositories. All other modules have been compacted into a single source repository. We have also updated the JVM to 21 and many libraries have been updated to address security and performance issues. See more information in the [v6.0.0 release notes](https://github.com/cBioPortal/cbioportal/releases/tag/v6.0.0).
* **Local Installations Feature**: When mutational signature data is loaded, show COSMIC reference signatures on the _Patient View_:
![image](https://github.com/cBioPortal/cbioportal/assets/1334004/10f73baa-d28c-4bb7-ad62-4751bd7f61cd)

## Dec 29, 2023
* **Added data** consisting of 5,120 samples from 13 studies:
* [Endometrial Cancer (MSK, Cancer Discovery 2023)](https://www.cbioportal.org/study/summary?id=ucec_ancestry_cds_msk_2023) *1882 samples*
Expand All @@ -16,6 +27,30 @@

* **Gene Tables Update:** Updated tables of genes (main and alias), based on [Oct 1, 2023 HGNC release](http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/). See seedDB release notes [here](https://github.com/cBioPortal/datahub/tree/master/seedDB#latest-seed-database-schema-2131) for details.

## Dec 5, 2023
* **New feature**: Filter by data types on the homepage:
![image](https://github.com/cBioPortal/cbioportal/assets/1334004/cf6d5486-bfd7-4f69-add0-442dbb4d354a)
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I'm not sure if this is specific to how I'm previewing it, but the image is showing up next to the text rather than under, which makes the vertical spacing funky. Can you make the image go under the text?

* **New feature**: Change colors of tracks in Oncoprint:
<img src="https://github.com/cBioPortal/cbioportal/assets/1334004/301b0efb-3063-44db-bc4c-86973e7c566a" width="700" />
* **New feature**: Show alteration frequencies per group in OncoPrint. [Example: RTK-RAS alterations in Smokers vs Never Smokers Lung Cancer Cases in MSK-IMPACT Clinical Sequencing Cohort](https://bit.ly/3PwKsDJ)
<img src="https://github.com/cBioPortal/cbioportal/assets/1334004/f2a9576e-c06d-447a-8eac-f0292bd1f935" width="700" />

## Oct 17, 2023
* **New feature**: Survival charts with landmark events and hazard ratios. [Example: TP53 in Lung Cancer Cases in MSK-IMPACT Clinical Sequencing Cohort](https://bit.ly/48QktxS)
<img src="https://github.com/cBioPortal/cbioportal/assets/1334004/dc97c3ae-ebd7-4cd3-bb76-165517c9d2ba" width="700" />
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Same thing, the preview is showing "Sequencing Cohort" as a second line of text along with the image, which means there's lots of vertical space between the first & second lines of text. Can you make the image go below all the text?


## Oct 3, 2023
* **New feature**: New Structural Variants Tab on _Results View_. [Example: TMPRSS2 Structural Variants in MSK-IMPACT Clinical Sequencing Cohort](https://bit.ly/49FDhRk)
<img src="https://github.com/cBioPortal/cbioportal/assets/1334004/141e2817-3300-4af2-a845-005403d75e74" width="700" />

## Sep 5, 2023
* **New feature**: Add gene-specific CNA charts to show all levels of copy number alterations (including gain and hetloss) on _Study View_:
<img src="https://github.com/cBioPortal/cbioportal/assets/1334004/873401ad-cbcf-4b07-9b80-8487af5abb18" width="700" />

## Aug 30, 2023
* **Enhancement**: Exclude a patient from your selection directly from the _Patient View_:
![image](https://github.com/cBioPortal/cbioportal/assets/1334004/501fe998-8408-48e3-a183-e27ab3ff3f28)

## Aug 21, 2023
* **Added data** consisting of 4,488 samples from 7 studies:
* [Lung Adenocarcinoma Met Organotropism (MSK, Cancer Cell 2023)](https://www.cbioportal.org/study/summary?id=luad_mskcc_2023_met_organotropism) *2653 samples*
Expand All @@ -39,10 +74,18 @@

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.

## Jul 18, 2023
* **New Feature**: Add mutations table and two-sided exact p-value to comparison. [Example: AR mutations in Primary vs Metastatic Prostate Cancer samples in MSK-IMPACT Clinical Sequencing Cohort](https://www.cbioportal.org/comparison/mutations?sessionId=5cf89323e4b0ab413787436c&groupOrder=%5B%22Primary%22%2C%22Metastasis%22%5D&selectedGene=AR)
<img src="https://github.com/cBioPortal/cbioportal/assets/1334004/da0cd1ef-b9b4-49f0-a9d3-42cff0204dc2" width="700" />


## 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 25, 2023
* **Local Installations Feature**: When custom driver annotations for structural variants are loaded, one can now filter by them in both the Oncoprint and the _Study View_.

## 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" />
Expand All @@ -69,13 +112,11 @@
<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)
* **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)
* **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
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