diff --git a/docs/News.md b/docs/News.md index 257defa35dd..903c745f93c 100644 --- a/docs/News.md +++ b/docs/News.md @@ -1,24 +1,23 @@ -## 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/). - - -## 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. - - - -## 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. +Screen Shot 2023-08-14 at 1 57 29 PM + + * 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. +Screen Shot 2023-08-14 at 4 26 22 PM + +## 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* @@ -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. - - - - This also allows to have numerical custom data after we query based on genes (custom data 2 in the image): - - - -## 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) - - -## 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) - - ## 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* @@ -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 - - -## 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: @@ -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 - - ## 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)