The goal of TCGAgistic is to easily load gistic copy-number analysis for TCGA cohorts into R
Install TCGAgistic from R universe:
# Install TCGAgistic from R:
install.packages('TCGAgistic', repos = c('https://ccicb.r-universe.dev', 'https://cloud.r-project.org'))Alternatively, you can install the development version from github:
# install.packages("remotes")
remotes::install_github('CCICB/TCGAgistic')Load the GISTIC dataset and visualise results
library(TCGAgistic)
library(maftools)
# Load dataset
gistic <- tcga_gistic_load("ACC", source = "Firehose", cnLevel = "all")
# Visualise results
gisticChromPlot(gistic)
library(TCGAgistic)
# Check available datasets
tcga_gistic_available()
#> Cohort FullName Source
#> 1 ACC Adrenocortical carcinoma Firehose
#> 2 ACC Adrenocortical carcinoma Firehose
#> 3 ACC Adrenocortical carcinoma Firehose
#> 4 BLCA Bladder urothelial carcinoma Firehose
#> 5 BLCA Bladder urothelial carcinoma Firehose
#> 6 BLCA Bladder urothelial carcinoma Firehose
#> 7 BRCA Breast invasive carcinoma Firehose
#> 8 BRCA Breast invasive carcinoma Firehose
#> 9 BRCA Breast invasive carcinoma Firehose
#> 10 CESC Cervical and endocervical cancers Firehose
#> 11 CESC Cervical and endocervical cancers Firehose
#> 12 CESC Cervical and endocervical cancers Firehose
#> 13 CHOL Cholangiocarcinoma Firehose
#> 14 CHOL Cholangiocarcinoma Firehose
#> 15 CHOL Cholangiocarcinoma Firehose
#> 16 COAD Colon adenocarcinoma Firehose
#> 17 COAD Colon adenocarcinoma Firehose
#> 18 COAD Colon adenocarcinoma Firehose
#> 19 COADREAD Colorectal adenocarcinoma Firehose
#> 20 COADREAD Colorectal adenocarcinoma Firehose
#> 21 COADREAD Colorectal adenocarcinoma Firehose
#> 22 DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma Firehose
#> 23 DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma Firehose
#> 24 DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma Firehose
#> 25 ESCA Esophageal carcinoma Firehose
#> 26 ESCA Esophageal carcinoma Firehose
#> 27 ESCA Esophageal carcinoma Firehose
#> 28 GBM Glioblastoma multiforme Firehose
#> 29 GBM Glioblastoma multiforme Firehose
#> 30 GBM Glioblastoma multiforme Firehose
#> 31 GBMLGG Glioma Firehose
#> 32 GBMLGG Glioma Firehose
#> 33 GBMLGG Glioma Firehose
#> 34 HNSC Head and Neck squamous cell carcinoma Firehose
#> 35 HNSC Head and Neck squamous cell carcinoma Firehose
#> 36 HNSC Head and Neck squamous cell carcinoma Firehose
#> 37 KICH Kidney Chromophobe Firehose
#> 38 KICH Kidney Chromophobe Firehose
#> 39 KICH Kidney Chromophobe Firehose
#> 40 KIPAN Pan-kidney cohort (KICH+KIRC+KIRP) Firehose
#> 41 KIPAN Pan-kidney cohort (KICH+KIRC+KIRP) Firehose
#> 42 KIPAN Pan-kidney cohort (KICH+KIRC+KIRP) Firehose
#> 43 KIRC Kidney renal clear cell carcinoma Firehose
#> 44 KIRC Kidney renal clear cell carcinoma Firehose
#> 45 KIRC Kidney renal clear cell carcinoma Firehose
#> 46 KIRP Kidney renal papillary cell carcinoma Firehose
#> 47 KIRP Kidney renal papillary cell carcinoma Firehose
#> 48 KIRP Kidney renal papillary cell carcinoma Firehose
#> 49 LAML Acute Myeloid Leukemia Firehose
#> 50 LAML Acute Myeloid Leukemia Firehose
#> 51 LAML Acute Myeloid Leukemia Firehose
#> 52 LGG Brain Lower Grade Glioma Firehose
#> 53 LGG Brain Lower Grade Glioma Firehose
#> 54 LGG Brain Lower Grade Glioma Firehose
#> 55 LIHC Liver hepatocellular carcinoma Firehose
#> 56 LIHC Liver hepatocellular carcinoma Firehose
#> 57 LIHC Liver hepatocellular carcinoma Firehose
#> 58 LUAD Lung adenocarcinoma Firehose
#> 59 LUAD Lung adenocarcinoma Firehose
#> 60 LUAD Lung adenocarcinoma Firehose
#> 61 LUSC Lung squamous cell carcinoma Firehose
#> 62 LUSC Lung squamous cell carcinoma Firehose
#> 63 LUSC Lung squamous cell carcinoma Firehose
#> 64 MESO Mesothelioma Firehose
#> 65 MESO Mesothelioma Firehose
#> 66 OV Ovarian serous cystadenocarcinoma Firehose
#> 67 OV Ovarian serous cystadenocarcinoma Firehose
#> 68 OV Ovarian serous cystadenocarcinoma Firehose
#> 69 PAAD Pancreatic adenocarcinoma Firehose
#> 70 PAAD Pancreatic adenocarcinoma Firehose
#> 71 PAAD Pancreatic adenocarcinoma Firehose
#> 72 PCPG Pheochromocytoma and Paraganglioma Firehose
#> 73 PCPG Pheochromocytoma and Paraganglioma Firehose
#> 74 PCPG Pheochromocytoma and Paraganglioma Firehose
#> 75 PRAD Prostate adenocarcinoma Firehose
#> 76 PRAD Prostate adenocarcinoma Firehose
#> 77 PRAD Prostate adenocarcinoma Firehose
#> 78 READ Rectum adenocarcinoma Firehose
#> 79 READ Rectum adenocarcinoma Firehose
#> 80 READ Rectum adenocarcinoma Firehose
#> 81 SARC Sarcoma Firehose
#> 82 SARC Sarcoma Firehose
#> 83 SARC Sarcoma Firehose
#> 84 SKCM Skin Cutaneous Melanoma Firehose
#> 85 SKCM Skin Cutaneous Melanoma Firehose
#> 86 SKCM Skin Cutaneous Melanoma Firehose
#> 87 STAD Stomach adenocarcinoma Firehose
#> 88 STAD Stomach adenocarcinoma Firehose
#> 89 STAD Stomach adenocarcinoma Firehose
#> 90 STES Stomach and Esophageal carcinoma Firehose
#> 91 STES Stomach and Esophageal carcinoma Firehose
#> 92 STES Stomach and Esophageal carcinoma Firehose
#> 93 TGCT Testicular Germ Cell Tumors Firehose
#> 94 TGCT Testicular Germ Cell Tumors Firehose
#> 95 TGCT Testicular Germ Cell Tumors Firehose
#> 96 THCA Thyroid carcinoma Firehose
#> 97 THCA Thyroid carcinoma Firehose
#> 98 THCA Thyroid carcinoma Firehose
#> 99 THYM Thymoma Firehose
#> 100 THYM Thymoma Firehose
#> 101 THYM Thymoma Firehose
#> 102 UCEC Uterine Corpus Endometrial Carcinoma Firehose
#> 103 UCEC Uterine Corpus Endometrial Carcinoma Firehose
#> 104 UCEC Uterine Corpus Endometrial Carcinoma Firehose
#> 105 UCS Uterine Carcinosarcoma Firehose
#> 106 UCS Uterine Carcinosarcoma Firehose
#> 107 UCS Uterine Carcinosarcoma Firehose
#> 108 UVM Uveal Melanoma Firehose
#> 109 UVM Uveal Melanoma Firehose
#> 110 UVM Uveal Melanoma Firehose
#> CopyNumberLevel Filepath DOI
#> 1 all ACC_Firehose.cnlevel_all.rds 10.7908/C1CN7372
#> 2 deep ACC_Firehose.cnlevel_deep.rds 10.7908/C1CN7372
#> 3 shallow ACC_Firehose.cnlevel_shallow.rds 10.7908/C1CN7372
#> 4 all BLCA_Firehose.cnlevel_all.rds 10.7908/C16T0KXB
#> 5 deep BLCA_Firehose.cnlevel_deep.rds 10.7908/C16T0KXB
#> 6 shallow BLCA_Firehose.cnlevel_shallow.rds 10.7908/C16T0KXB
#> 7 all BRCA_Firehose.cnlevel_all.rds 10.7908/C1NP23RQ
#> 8 deep BRCA_Firehose.cnlevel_deep.rds 10.7908/C1NP23RQ
#> 9 shallow BRCA_Firehose.cnlevel_shallow.rds 10.7908/C1NP23RQ
#> 10 all CESC_Firehose.cnlevel_all.rds 10.7908/C16D5SCD
#> 11 deep CESC_Firehose.cnlevel_deep.rds 10.7908/C16D5SCD
#> 12 shallow CESC_Firehose.cnlevel_shallow.rds 10.7908/C16D5SCD
#> 13 all CHOL_Firehose.cnlevel_all.rds 10.7908/C1S181WN
#> 14 deep CHOL_Firehose.cnlevel_deep.rds 10.7908/C1S181WN
#> 15 shallow CHOL_Firehose.cnlevel_shallow.rds 10.7908/C1S181WN
#> 16 all COAD_Firehose.cnlevel_all.rds 10.7908/C1M61JMS
#> 17 deep COAD_Firehose.cnlevel_deep.rds 10.7908/C1M61JMS
#> 18 shallow COAD_Firehose.cnlevel_shallow.rds 10.7908/C1M61JMS
#> 19 all COADREAD_Firehose.cnlevel_all.rds 10.7908/C1SJ1JZ8
#> 20 deep COADREAD_Firehose.cnlevel_deep.rds 10.7908/C1SJ1JZ8
#> 21 shallow COADREAD_Firehose.cnlevel_shallow.rds 10.7908/C1SJ1JZ8
#> 22 all DLBC_Firehose.cnlevel_all.rds 10.7908/C13R0S77
#> 23 deep DLBC_Firehose.cnlevel_deep.rds 10.7908/C13R0S77
#> 24 shallow DLBC_Firehose.cnlevel_shallow.rds 10.7908/C13R0S77
#> 25 all ESCA_Firehose.cnlevel_all.rds 10.7908/C1XS5TQM
#> 26 deep ESCA_Firehose.cnlevel_deep.rds 10.7908/C1XS5TQM
#> 27 shallow ESCA_Firehose.cnlevel_shallow.rds 10.7908/C1XS5TQM
#> 28 all GBM_Firehose.cnlevel_all.rds 10.7908/C1HD7V19
#> 29 deep GBM_Firehose.cnlevel_deep.rds 10.7908/C1HD7V19
#> 30 shallow GBM_Firehose.cnlevel_shallow.rds 10.7908/C1HD7V19
#> 31 all GBMLGG_Firehose.cnlevel_all.rds 10.7908/C1K35T1N
#> 32 deep GBMLGG_Firehose.cnlevel_deep.rds 10.7908/C1K35T1N
#> 33 shallow GBMLGG_Firehose.cnlevel_shallow.rds 10.7908/C1K35T1N
#> 34 all HNSC_Firehose.cnlevel_all.rds 10.7908/C1V987FP
#> 35 deep HNSC_Firehose.cnlevel_deep.rds 10.7908/C1V987FP
#> 36 shallow HNSC_Firehose.cnlevel_shallow.rds 10.7908/C1V987FP
#> 37 all KICH_Firehose.cnlevel_all.rds 10.7908/C1DZ07QR
#> 38 deep KICH_Firehose.cnlevel_deep.rds 10.7908/C1DZ07QR
#> 39 shallow KICH_Firehose.cnlevel_shallow.rds 10.7908/C1DZ07QR
#> 40 all KIPAN_Firehose.cnlevel_all.rds 10.7908/C1CR5SSS
#> 41 deep KIPAN_Firehose.cnlevel_deep.rds 10.7908/C1CR5SSS
#> 42 shallow KIPAN_Firehose.cnlevel_shallow.rds 10.7908/C1CR5SSS
#> 43 all KIRC_Firehose.cnlevel_all.rds 10.7908/C1FF3RRP
#> 44 deep KIRC_Firehose.cnlevel_deep.rds 10.7908/C1FF3RRP
#> 45 shallow KIRC_Firehose.cnlevel_shallow.rds 10.7908/C1FF3RRP
#> 46 all KIRP_Firehose.cnlevel_all.rds 10.7908/C1H41QVC
#> 47 deep KIRP_Firehose.cnlevel_deep.rds 10.7908/C1H41QVC
#> 48 shallow KIRP_Firehose.cnlevel_shallow.rds 10.7908/C1H41QVC
#> 49 all LAML_Firehose.cnlevel_all.rds 10.7908/C16H4GT5
#> 50 deep LAML_Firehose.cnlevel_deep.rds 10.7908/C16H4GT5
#> 51 shallow LAML_Firehose.cnlevel_shallow.rds 10.7908/C16H4GT5
#> 52 all LGG_Firehose.cnlevel_all.rds 10.7908/C12J6B7R
#> 53 deep LGG_Firehose.cnlevel_deep.rds 10.7908/C12J6B7R
#> 54 shallow LGG_Firehose.cnlevel_shallow.rds 10.7908/C12J6B7R
#> 55 all LIHC_Firehose.cnlevel_all.rds 10.7908/C1474990
#> 56 deep LIHC_Firehose.cnlevel_deep.rds 10.7908/C1474990
#> 57 shallow LIHC_Firehose.cnlevel_shallow.rds 10.7908/C1474990
#> 58 all LUAD_Firehose.cnlevel_all.rds 10.7908/C1348JSB
#> 59 deep LUAD_Firehose.cnlevel_deep.rds 10.7908/C1348JSB
#> 60 shallow LUAD_Firehose.cnlevel_shallow.rds 10.7908/C1348JSB
#> 61 all LUSC_Firehose.cnlevel_all.rds 10.7908/C1RJ4HX7
#> 62 deep LUSC_Firehose.cnlevel_deep.rds 10.7908/C1RJ4HX7
#> 63 shallow LUSC_Firehose.cnlevel_shallow.rds 10.7908/C1RJ4HX7
#> 64 all MESO_Firehose.cnlevel_all.rds 10.7908/C1DZ07R6
#> 65 shallow MESO_Firehose.cnlevel_shallow.rds 10.7908/C1DZ07R6
#> 66 all OV_Firehose.cnlevel_all.rds 10.7908/C1P84B9Q
#> 67 deep OV_Firehose.cnlevel_deep.rds 10.7908/C1P84B9Q
#> 68 shallow OV_Firehose.cnlevel_shallow.rds 10.7908/C1P84B9Q
#> 69 all PAAD_Firehose.cnlevel_all.rds 10.7908/C1BP0271
#> 70 deep PAAD_Firehose.cnlevel_deep.rds 10.7908/C1BP0271
#> 71 shallow PAAD_Firehose.cnlevel_shallow.rds 10.7908/C1BP0271
#> 72 all PCPG_Firehose.cnlevel_all.rds 10.7908/C19K49PX
#> 73 deep PCPG_Firehose.cnlevel_deep.rds 10.7908/C19K49PX
#> 74 shallow PCPG_Firehose.cnlevel_shallow.rds 10.7908/C19K49PX
#> 75 all PRAD_Firehose.cnlevel_all.rds 10.7908/C14Q7TFZ
#> 76 deep PRAD_Firehose.cnlevel_deep.rds 10.7908/C14Q7TFZ
#> 77 shallow PRAD_Firehose.cnlevel_shallow.rds 10.7908/C14Q7TFZ
#> 78 all READ_Firehose.cnlevel_all.rds 10.7908/C1ZS2VZB
#> 79 deep READ_Firehose.cnlevel_deep.rds 10.7908/C1ZS2VZB
#> 80 shallow READ_Firehose.cnlevel_shallow.rds 10.7908/C1ZS2VZB
#> 81 all SARC_Firehose.cnlevel_all.rds 10.7908/C190238F
#> 82 deep SARC_Firehose.cnlevel_deep.rds 10.7908/C190238F
#> 83 shallow SARC_Firehose.cnlevel_shallow.rds 10.7908/C190238F
#> 84 all SKCM_Firehose.cnlevel_all.rds 10.7908/C1445KXQ
#> 85 deep SKCM_Firehose.cnlevel_deep.rds 10.7908/C1445KXQ
#> 86 shallow SKCM_Firehose.cnlevel_shallow.rds 10.7908/C1445KXQ
#> 87 all STAD_Firehose.cnlevel_all.rds 10.7908/C1K073R3
#> 88 deep STAD_Firehose.cnlevel_deep.rds 10.7908/C1K073R3
#> 89 shallow STAD_Firehose.cnlevel_shallow.rds 10.7908/C1K073R3
#> 90 all STES_Firehose.cnlevel_all.rds 10.7908/C1D50MFS
#> 91 deep STES_Firehose.cnlevel_deep.rds 10.7908/C1D50MFS
#> 92 shallow STES_Firehose.cnlevel_shallow.rds 10.7908/C1D50MFS
#> 93 all TGCT_Firehose.cnlevel_all.rds 10.7908/C1ZS2W06
#> 94 deep TGCT_Firehose.cnlevel_deep.rds 10.7908/C1ZS2W06
#> 95 shallow TGCT_Firehose.cnlevel_shallow.rds 10.7908/C1ZS2W06
#> 96 all THCA_Firehose.cnlevel_all.rds 10.7908/C1SX6CQR
#> 97 deep THCA_Firehose.cnlevel_deep.rds 10.7908/C1SX6CQR
#> 98 shallow THCA_Firehose.cnlevel_shallow.rds 10.7908/C1SX6CQR
#> 99 all THYM_Firehose.cnlevel_all.rds 10.7908/C1CJ8D00
#> 100 deep THYM_Firehose.cnlevel_deep.rds 10.7908/C1CJ8D00
#> 101 shallow THYM_Firehose.cnlevel_shallow.rds 10.7908/C1CJ8D00
#> 102 all UCEC_Firehose.cnlevel_all.rds 10.7908/C16M36B7
#> 103 deep UCEC_Firehose.cnlevel_deep.rds 10.7908/C16M36B7
#> 104 shallow UCEC_Firehose.cnlevel_shallow.rds 10.7908/C16M36B7
#> 105 all UCS_Firehose.cnlevel_all.rds 10.7908/C1W37VTX
#> 106 deep UCS_Firehose.cnlevel_deep.rds 10.7908/C1W37VTX
#> 107 shallow UCS_Firehose.cnlevel_shallow.rds 10.7908/C1W37VTX
#> 108 all UVM_Firehose.cnlevel_all.rds 10.7908/C1TX3DWK
#> 109 deep UVM_Firehose.cnlevel_deep.rds 10.7908/C1TX3DWK
#> 110 shallow UVM_Firehose.cnlevel_shallow.rds 10.7908/C1TX3DWKTCGAgistic streams rds files from github, located in the
TCGAgisticDB package, into your
local R session