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Cbioportal Cnv

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Laatst bijgewerkt: 2022-02-05 07:58:49

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Toegevoegd door: Rob Pierce

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cBioPortal for Cancer Genomics

Colorectal Adenocarcinoma Triplets (MSKCC, Genome Biol 2014) 138 samples. Colorectal Cancer (MSK, Gastroenterology 2020) 471 samples. Disparities in metastatic colorectal cancer between Africans and Americans (MSK, 2020) 64 …
Url: http://www.cbioportal.org/
cBioPortal for Cancer Genomics

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Toegevoegd door: Joshua Pryor

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cBioPortalData: User Start Guide - Bioconductor

26-10-2021 · The cBioPortal for Cancer Genomics website is a great resource for interactive exploration of study datasets. However, it does not easily allow the analyst to obtain and further analyze the data. We’ve developed the cBioPortalData package to fill this need to programmatically access the data resources available on the cBioPortal.
Url: https://www.bioconductor.org/packages/release/bioc//vignettes/cBioPortalData/inst/doc/cBioPortalData.html
cBioPortalData: User Start Guide - Bioconductor

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Toegevoegd door: Mouhamad El Ramlawi

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The CNVs’ status were analyzed using cBioPortal database

The CNVs’ status were analyzed using cBioPortal database (http://www.cbioportal.org/) and COSMIC dataset (V74). The cBioPortal database which is developed by Memorial Sloan Kettering Cancer Center (MSK). It is a comprehensive and widely-used platform that allows data mining, data integration based on the TCGA database.
Url: https://www.thno.org/v10/p10823/thnov10p10823s1.pdf
The CNVs’ status were analyzed using cBioPortal database

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Toegevoegd door: Dale Exon

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Frequently Asked Questions - cBioPortal

the goal of cbioportal is to significantly lower the barriers between complex genomic data and cancer researchers by providing rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics projects, and therefore to empower researchers to translate these rich data sets into biologic …
Url: https://docs.cbioportal.org/1.-general/faq
Frequently Asked Questions - cBioPortal

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Toegevoegd door: Lauren Pullock

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Downloads - cBioPortal

Study staging files. Staging files for the studies on cbioportal.org can be download from the Datasets Page. These studies can be validated and loaded in a local cBioPortal instances using the validator and importer. Any issues with a downloaded …
Url: https://docs.cbioportal.org/5.2-datasets/downloads
Downloads - cBioPortal

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Toegevoegd door: Sam Althorpe

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File Formats - cBioPortal

By default, cBioPortal filters out Silent, Intron, IGR, 3'UTR, 5'UTR, 3'Flank and 5'Flank, except for the promoter mutations of the TERT gene. For no filtering, include this field in the metadata file, but leave it empty. For cBioPortal default filtering, do not include this field in the metadata file.
Url: https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats
File Formats - cBioPortal

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Toegevoegd door: Tony Efstathiou

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RNA expression — CNVkit 0.9.8 documentation

CNV-expression correlation coefficients – calculated per gene via the script cnv_expression_correlate.py included with CNVkit. A pre-calculated set of coefficients calculated on TCGA melanoma datasets, obtained from cBioPortal, is bundled with CNVkit under data/tcga-skcm.cnv-expr-corr.tsv.
Url: https://cnvkit.readthedocs.io/en/stable/rna.html
RNA expression — CNVkit 0.9.8 documentation

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Toegevoegd door: Bradley Pinches

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X-CNV: genome-wide prediction of the pathogenicity of copy ...

18-08-2021 · X-CNV has a unique ability to integrate diverse human genome information towards a quantitative measure of CNV pathogenicity on the whole genome-scale. X-CNV created a curated benchmark CNV list by combining publicly available CNV resources to generate the most comprehensive list of feature-related CNV pathogenicity.
Url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8375180/
X-CNV: genome-wide prediction of the pathogenicity of copy ...

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Toegevoegd door: Ashlie Webb

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cBioPortal for Cancer Genomics

TCGA Breast Invasive Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. Summary. Clinical Data. Heatmaps. CN Segments. KM Plot: Overall Survival (months) 0 50 100 150 200 250 0% 50% 100% KM Plot: Overall Survival (months) All patients.
Url: https://www.cbioportal.org/study/summary?id=brca_tcga
cBioPortal for Cancer Genomics

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Toegevoegd door: cBioPortal

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cBioPortal Webinar 1: Introduction

cBioPortal Webinar 1: Introduction

Toegevoegd door: cBioPortal

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cBioPortal Webinar 2: Mutation Details & Patient View

cBioPortal Webinar 2: Mutation Details & Patient View

Toegevoegd door: Cholangiocarcinoma Foundation

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ICRN: Introduction to cBioPortal for Cancer Genomics

ICRN: Introduction to cBioPortal for Cancer Genomics

Toegevoegd door: Farhan Haq

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Cancer Genomics (Part 3): Easy guide to access RNA sequencing data of cancer (Example: Cbioportal)

Cancer Genomics (Part 3): Easy guide to access RNA sequencing data of cancer (Example: Cbioportal)

Toegevoegd door: cBioPortal

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cBioPortal: Comparing samples based on expression level of a gene

cBioPortal: Comparing samples based on expression level of a gene

Toegevoegd door: Cristi Vlad

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Cbioportal - Tool for Cancer Genomics Analysis [Overview]

Cbioportal - Tool for Cancer Genomics Analysis [Overview]

Toegevoegd door: cBioPortal

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cBioPortal Webinar 4: Group Comparison

cBioPortal Webinar 4: Group Comparison

Toegevoegd door: cBioPortal

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cBioPortal Webinar 5: API & R Client

cBioPortal Webinar 5: API & R Client

Toegevoegd door: cBioPortal

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cBioPortal: Filtering and adding clinical data to Mutations tab

cBioPortal: Filtering and adding clinical data to Mutations tab

Toegevoegd door: IUSM-CCBB

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B4B: Module 5 - CBioportal

B4B: Module 5 - CBioportal
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