curatedTCGAData-package: curatedTCGAData-package
In waldronlab/curatedTCGAData: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
curatedTCGAData-package R Documentation
curatedTCGAData-package
Description
The curatedTCGAData package provides a convenient and user-friendly
interface for The Cancer Genome Atlas data from the Firehose GDAC Pipeline.
Please note that _most_ of the data from the GDAC Firehose pipeline uses
the 'hg19' reference genome (except for a few cancers; refer to
https://confluence.broadinstitute.org/display/GDAC/FAQ).
It is highly recommended to use the 'TCGAutils' companion package.
It provides convenience functions for manipulating curatedTCGAData objects.
See package for more details
(http://bioconductor.org/packages/TCGAutils).
diseaseCodes
The following are the TCGA disease codes and full names as posted on the
official website
(https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations).
Study Abbreviation Study Name
---------------------------------------------------------------------------
1 ACC Adrenocortical Carcinoma
2 BLCA Bladder Urothelial Carcinoma
3 BRCA Breast Invasive Carcinoma
4 CESC Cervical Squamous Cell Carcinoma And Endocervical Adenocarcinoma
5 CHOL Cholangiocarcinoma
6 CNTL Controls
7 COAD Colon Adenocarcinoma
8 DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
9 ESCA Esophageal Carcinoma
10 GBM Glioblastoma Multiforme
11 HNSC Head And Neck Squamous Cell Carcinoma
12 KICH Kidney Chromophobe
13 KIRC Kidney Renal Clear Cell Carcinoma
14 KIRP Kidney Renal Papillary Cell Carcinoma
15 LAML Acute Myeloid Leukemia
16 LGG Brain Lower Grade Glioma
17 LIHC Liver Hepatocellular Carcinoma
18 LUAD Lung Adenocarcinoma
19 LUSC Lung Squamous Cell Carcinoma
20 MESO Mesothelioma
21 OV Ovarian Serous Cystadenocarcinoma
22 PAAD Pancreatic Adenocarcinoma
23 PCPG Pheochromocytoma And Paraganglioma
24 PRAD Prostate Adenocarcinoma
25 READ Rectum Adenocarcinoma
26 SARC Sarcoma
27 SKCM Skin Cutaneous Melanoma
28 STAD Stomach Adenocarcinoma
29 TGCT Testicular Germ Cell Tumors
30 THCA Thyroid Carcinoma
31 THYM Thymoma
32 UCEC Uterine Corpus Endometrial Carcinoma
33 UCS Uterine Carcinosarcoma
34 UVM Uveal Melanoma
Author(s)
Maintainer: Marcel Ramos marcel.ramos@roswellpark.org (ORCID)
Other contributors:
Levi Waldron lwaldron.research@gmail.com [contributor]
Lucas Schiffer schiffer.lucas@gmail.com [contributor]
Ludwig Geistlinger ludwig.geistlinger@sph.cuny.edu [contributor]
Valerie Obenchain valerie.obenchain@roswellpark.org [contributor]
Martin Morgan martin.morgan@roswellpark.org [contributor]
See Also
Useful links:
Report bugs at https://github.com/waldronlab/curatedTCGAData/issues
Examples
help(package = "curatedTCGAData")
waldronlab/curatedTCGAData documentation built on Feb. 7, 2024, 1:12 p.m.
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| curatedTCGAData-package | R Documentation |
curatedTCGAData-package
Description
The curatedTCGAData package provides a convenient and user-friendly interface for The Cancer Genome Atlas data from the Firehose GDAC Pipeline. Please note that _most_ of the data from the GDAC Firehose pipeline uses the 'hg19' reference genome (except for a few cancers; refer to https://confluence.broadinstitute.org/display/GDAC/FAQ).
It is highly recommended to use the 'TCGAutils' companion package. It provides convenience functions for manipulating curatedTCGAData objects. See package for more details (http://bioconductor.org/packages/TCGAutils).
diseaseCodes
The following are the TCGA disease codes and full names as posted on the official website (https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations).
Study Abbreviation Study Name --------------------------------------------------------------------------- 1 ACC Adrenocortical Carcinoma 2 BLCA Bladder Urothelial Carcinoma 3 BRCA Breast Invasive Carcinoma 4 CESC Cervical Squamous Cell Carcinoma And Endocervical Adenocarcinoma 5 CHOL Cholangiocarcinoma 6 CNTL Controls 7 COAD Colon Adenocarcinoma 8 DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma 9 ESCA Esophageal Carcinoma 10 GBM Glioblastoma Multiforme 11 HNSC Head And Neck Squamous Cell Carcinoma 12 KICH Kidney Chromophobe 13 KIRC Kidney Renal Clear Cell Carcinoma 14 KIRP Kidney Renal Papillary Cell Carcinoma 15 LAML Acute Myeloid Leukemia 16 LGG Brain Lower Grade Glioma 17 LIHC Liver Hepatocellular Carcinoma 18 LUAD Lung Adenocarcinoma 19 LUSC Lung Squamous Cell Carcinoma 20 MESO Mesothelioma 21 OV Ovarian Serous Cystadenocarcinoma 22 PAAD Pancreatic Adenocarcinoma 23 PCPG Pheochromocytoma And Paraganglioma 24 PRAD Prostate Adenocarcinoma 25 READ Rectum Adenocarcinoma 26 SARC Sarcoma 27 SKCM Skin Cutaneous Melanoma 28 STAD Stomach Adenocarcinoma 29 TGCT Testicular Germ Cell Tumors 30 THCA Thyroid Carcinoma 31 THYM Thymoma 32 UCEC Uterine Corpus Endometrial Carcinoma 33 UCS Uterine Carcinosarcoma 34 UVM Uveal Melanoma
Author(s)
Maintainer: Marcel Ramos marcel.ramos@roswellpark.org (ORCID)
Other contributors:
Levi Waldron lwaldron.research@gmail.com [contributor]
Lucas Schiffer schiffer.lucas@gmail.com [contributor]
Ludwig Geistlinger ludwig.geistlinger@sph.cuny.edu [contributor]
Valerie Obenchain valerie.obenchain@roswellpark.org [contributor]
Martin Morgan martin.morgan@roswellpark.org [contributor]
See Also
Useful links:
Report bugs at https://github.com/waldronlab/curatedTCGAData/issues
Examples
help(package = "curatedTCGAData")
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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