diff --git a/articles/MultiAssayExperiment_Analysis.html b/articles/MultiAssayExperiment_Analysis.html index 1876b88..25ee684 100644 --- a/articles/MultiAssayExperiment_Analysis.html +++ b/articles/MultiAssayExperiment_Analysis.html @@ -109,7 +109,7 @@

Marcel NY

Levi Waldron

- CUNY School of Public Health, New York, NY

September 26, 2023

+ CUNY School of Public Health, New York, NY

November 21, 2023

Source: vignettes/MultiAssayExperiment_Analysis.Rmd diff --git a/articles/Ramos_MultiAssayExperiment.html b/articles/Ramos_MultiAssayExperiment.html index 1127413..e1d1ee1 100644 --- a/articles/Ramos_MultiAssayExperiment.html +++ b/articles/Ramos_MultiAssayExperiment.html @@ -109,7 +109,7 @@

Marcel NY

Levi Waldron

- CUNY School of Public Health, New York, NY

September 26, 2023

+ CUNY School of Public Health, New York, NY

November 21, 2023

Source: vignettes/Ramos_MultiAssayExperiment.Rmd @@ -1009,40 +1009,40 @@

Listing the studies available
 cbio <- cBioPortal()
 getStudies(cbio)
-
## # A tibble: 391 × 13
+
## # A tibble: 393 × 13
 ##    name          description publicStudy groups status importDate allSampleCount
 ##    <chr>         <chr>       <lgl>       <chr>   <int> <chr>               <int>
 ##  1 Adrenocortic… "TCGA Adre… TRUE        PUBLIC      0 2023-06-1…             92
 ##  2 Acute Myeloi… "TCGA Acut… TRUE        PUBLIC      0 2023-06-1…            200
 ##  3 Bladder Urot… "TCGA Blad… TRUE        PUBLIC      0 2023-06-1…            413
-##  4 Breast Invas… "TCGA Brea… TRUE        PUBLIC      0 2023-06-1…           1108
-##  5 Kidney Renal… "TCGA Kidn… TRUE        PUBLIC      0 2023-06-1…            538
-##  6 Cervical Squ… "TCGA Cerv… TRUE        PUBLIC      0 2023-06-1…            310
-##  7 Cholangiocar… "TCGA Chol… TRUE        PUBLIC      0 2023-06-1…             51
-##  8 Kidney Chrom… "TCGA Kidn… TRUE        PUBLIC      0 2023-06-1…            113
-##  9 Colorectal A… "TCGA Colo… TRUE        PUBLIC      0 2023-06-1…            640
-## 10 Lymphoid Neo… "TCGA Lymp… TRUE        PUBLIC      0 2023-06-1…             48
-## # ℹ 381 more rows
+##  4 Kidney Renal… "TCGA Kidn… TRUE        PUBLIC      0 2023-06-1…            538
+##  5 Cervical Squ… "TCGA Cerv… TRUE        PUBLIC      0 2023-06-1…            310
+##  6 Cholangiocar… "TCGA Chol… TRUE        PUBLIC      0 2023-06-1…             51
+##  7 Kidney Chrom… "TCGA Kidn… TRUE        PUBLIC      0 2023-06-1…            113
+##  8 Colorectal A… "TCGA Colo… TRUE        PUBLIC      0 2023-06-1…            640
+##  9 Lymphoid Neo… "TCGA Lymp… TRUE        PUBLIC      0 2023-06-1…             48
+## 10 Esophageal C… "TCGA Esop… TRUE        PUBLIC      0 2023-06-1…            186
+## # ℹ 383 more rows
 ## # ℹ 6 more variables: readPermission <lgl>, studyId <chr>, cancerTypeId <chr>,
 ## #   referenceGenome <chr>, pmid <chr>, citation <chr>

 
We can also see the build status of the datasets using the
 buildReport argument.

 
 getStudies(cbio, buildReport = TRUE)

-
## # A tibble: 391 × 15
+
## # A tibble: 393 × 15
 ##    name          description publicStudy groups status importDate allSampleCount
 ##    <chr>         <chr>       <lgl>       <chr>   <int> <chr>               <int>
 ##  1 Adrenocortic… "TCGA Adre… TRUE        PUBLIC      0 2023-06-1…             92
 ##  2 Acute Myeloi… "TCGA Acut… TRUE        PUBLIC      0 2023-06-1…            200
 ##  3 Bladder Urot… "TCGA Blad… TRUE        PUBLIC      0 2023-06-1…            413
-##  4 Breast Invas… "TCGA Brea… TRUE        PUBLIC      0 2023-06-1…           1108
-##  5 Kidney Renal… "TCGA Kidn… TRUE        PUBLIC      0 2023-06-1…            538
-##  6 Cervical Squ… "TCGA Cerv… TRUE        PUBLIC      0 2023-06-1…            310
-##  7 Cholangiocar… "TCGA Chol… TRUE        PUBLIC      0 2023-06-1…             51
-##  8 Kidney Chrom… "TCGA Kidn… TRUE        PUBLIC      0 2023-06-1…            113
-##  9 Colorectal A… "TCGA Colo… TRUE        PUBLIC      0 2023-06-1…            640
-## 10 Lymphoid Neo… "TCGA Lymp… TRUE        PUBLIC      0 2023-06-1…             48
-## # ℹ 381 more rows
+##  4 Kidney Renal… "TCGA Kidn… TRUE        PUBLIC      0 2023-06-1…            538
+##  5 Cervical Squ… "TCGA Cerv… TRUE        PUBLIC      0 2023-06-1…            310
+##  6 Cholangiocar… "TCGA Chol… TRUE        PUBLIC      0 2023-06-1…             51
+##  7 Kidney Chrom… "TCGA Kidn… TRUE        PUBLIC      0 2023-06-1…            113
+##  8 Colorectal A… "TCGA Colo… TRUE        PUBLIC      0 2023-06-1…            640
+##  9 Lymphoid Neo… "TCGA Lymp… TRUE        PUBLIC      0 2023-06-1…             48
+## 10 Esophageal C… "TCGA Esop… TRUE        PUBLIC      0 2023-06-1…            186
+## # ℹ 383 more rows
 ## # ℹ 8 more variables: readPermission <lgl>, studyId <chr>, cancerTypeId <chr>,
 ## #   referenceGenome <chr>, pmid <chr>, citation <chr>, api_build <lgl>,
 ## #   pack_build <lgl>

@@ -1058,18 +1058,17 @@ 
cBioDataPacklibrary(cBioPortalData)
 
 (uvm <- cBioDataPack("uvm_tcga"))

-
## A MultiAssayExperiment object of 9 listed
+
## A MultiAssayExperiment object of 8 listed
 ##  experiments with user-defined names and respective classes.
-##  Containing an ExperimentList class object of length 9:
+##  Containing an ExperimentList class object of length 8:
 ##  [1] cna_hg19.seg: RaggedExperiment with 7618 rows and 80 columns
-##  [2] CNA: SummarizedExperiment with 24776 rows and 80 columns
-##  [3] linear_CNA: SummarizedExperiment with 24776 rows and 80 columns
-##  [4] methylation_hm450: SummarizedExperiment with 15469 rows and 80 columns
-##  [5] mutations_extended: RaggedExperiment with 2174 rows and 80 columns
-##  [6] mutations_mskcc: RaggedExperiment with 2174 rows and 80 columns
-##  [7] RNA_Seq_v2_expression_median: SummarizedExperiment with 20531 rows and 80 columns
-##  [8] RNA_Seq_v2_mRNA_median_all_sample_Zscores: SummarizedExperiment with 20531 rows and 80 columns
-##  [9] RNA_Seq_v2_mRNA_median_Zscores: SummarizedExperiment with 20440 rows and 80 columns
+##  [2] cna: SummarizedExperiment with 24776 rows and 80 columns
+##  [3] linear_cna: SummarizedExperiment with 24776 rows and 80 columns
+##  [4] methylation_hm450: SummarizedExperiment with 15468 rows and 80 columns
+##  [5] mrna_seq_v2_rsem_zscores_ref_all_samples: SummarizedExperiment with 20531 rows and 80 columns
+##  [6] mrna_seq_v2_rsem_zscores_ref_diploid_samples: SummarizedExperiment with 20440 rows and 80 columns
+##  [7] mrna_seq_v2_rsem: SummarizedExperiment with 20531 rows and 80 columns
+##  [8] mutations: RaggedExperiment with 2174 rows and 80 columns
 ## Functionality:
 ##  experiments() - obtain the ExperimentList instance
 ##  colData() - the primary/phenotype DataFrame
diff --git a/articles/cBioPortal_Studies.html b/articles/cBioPortal_Studies.html
index a9bbc92..d98c233 100644
--- a/articles/cBioPortal_Studies.html
+++ b/articles/cBioPortal_Studies.html
@@ -318,55 +318,6 @@ 
cBioPortalData() && cBioDataPack()<
 
 
 
-Breast Invasive Carcinoma (TCGA, Firehose Legacy)
-
-
-TCGA Breast Invasive Carcinoma. Source data from
-GDAC
-Firehose. Previously known as TCGA Provisional.
-
-
-TRUE
-
-
-PUBLIC
-
-
-0
-
-
-2023-06-19 09:47:32
-
-
-1108
-
-
-TRUE
-
-
-brca_tcga
-
-
-brca
-
-
-hg19
-
-
-NA
-
-
-NA
-
-
-TRUE
-
-
-TRUE
-
-
-
-
 Kidney Renal Clear Cell Carcinoma (TCGA, Firehose Legacy)
 
 
@@ -2942,54 +2893,6 @@ 
cBioPortalData() && cBioDataPack()<
 
 
 
-Urothelial Carcinoma (BCAN/HCRN, 2022)
-
-
-UC-GENOME: Urothelial Cancer-GENOmic analysis to iMprove patient
-outcomes and rEsearch.
-
-
-TRUE
-
-
-UCGENOME_BCAN_HCRN_2015
-
-
-0
-
-
-2023-06-19 14:31:55
-
-
-192
-
-
-TRUE
-
-
-blca_bcan_hcrn_2022
-
-
-blca
-
-
-hg19
-
-
-NA
-
-
-NA
-
-
-FALSE
-
-
-TRUE
-
-
-
-
 Pediatric Brain Cancer (CPTAC/CHOP, Cell 2020)
 
 
@@ -10089,54 +9992,6 @@ 
cBioPortalData() && cBioDataPack()<
 
 
 
-Non-Small Cell Lung Cancer (MSK, Science 2015)
-
-
-Whole-exome sequencing of tumor-normal tissue pairs from 16 non-small
-cell lung cancer samples.
-
-
-TRUE
-
-
-PUBLIC
-
-
-0
-
-
-2023-06-20 12:45:01
-
-
-16
-
-
-TRUE
-
-
-nsclc_mskcc_2015
-
-
-nsclc
-
-
-hg19
-
-
-25765070
-
-
-Rivzi et al. Science 2016
-
-
-TRUE
-
-
-TRUE
-
-
-
-
 Prostate Cancer (MSK, Cell Metab 2020)
 
 
@@ -12663,53 +12518,6 @@ 
cBioPortalData() && cBioDataPack()<
 
 
 
-Mature T and NK Neoplasms (MSK, 2022)
-
-
-Targeted sequencing of 132 Mature T and NK Neoplasms and their matched
-normals via MSK-IMPACT.
-
-
-TRUE
-
-
-
-
-0
-
-
-2023-06-21 14:17:35
-
-
-132
-
-
-TRUE
-
-
-mtnn_msk_2022
-
-
-mtnn
-
-
-hg19
-
-
-NA
-
-
-NA
-
-
-FALSE
-
-
-FALSE
-
-
-
-
 Radiation-associated Sarcomas (MSK, 2023)
 
 
@@ -15427,53 +15235,6 @@ 
cBioPortalData() && cBioDataPack()<
 
 
 
-Cervical Cancer (MSK, 2023)
-
-
-Targeted Sequencing of 177 cervical tumors and their matched normal
-samples via MSK-IMPACT.
-
-
-TRUE
-
-
-
-
-0
-
-
-2023-07-24 16:03:07
-
-
-177
-
-
-TRUE
-
-
-cervix_msk_2023
-
-
-cervix
-
-
-hg19
-
-
-NA
-
-
-NA
-
-
-NA
-
-
-NA
-
-
-
-
 Prostate Adenocarcinoma (Broad/Cornell, Cell 2013)
 
 
@@ -18707,24 +18468,13 @@ 
cBioPortalData() && cBioDataPack()<
 
 
 
-MSK MetTropism (MSK, Cell 2021)
+Metastatic Non-Small Cell Lung Cancer (MSK, Nature Medicine 2022)
 
 
-MSK-MET (Memorial Sloan Kettering - Metastatic Events and Tropisms) is
-an integrated pan-cancer cohort of tumor genomic and clinical outcome
-data from 25,000 patients. We analyzed this dataset to identify
-associations between tumor genomic alterations and patterns of
-metastatic dissemination across 50 tumor types. We found that
-chromosomal instability is strongly correlated with metastatic burden in
-some tumor types, including prostate adenocarcinoma, lung adenocarcinoma
-and HR+/HER2+ breast ductal carcinoma, but not in others, such as
-colorectal MSS, pancreatic adenocarcinoma and high-grade serous ovarian
-cancer. We also identified specific somatic alterations associated with
-increased metastatic burden and specific routes of metastatic spread.
-Our data offer a unique resource for the investigation of the biologic
-basis for metastatic spread and highlight the crucial role of
-chromosomal instability in cancer progression.
-PubMed
+Targeted sequencing of ctDNA samples drawn from patients with metastatic
+NSCLC using the Resolution ctDx Lung platform. For more information
+contact 
+or 
 
 
 TRUE
@@ -18735,28 +18485,28 @@ 
cBioPortalData() && cBioDataPack()<
 0
 
 
-2023-08-16 20:03:15
+2023-08-16 22:58:19
 
 
-25775
+2621
 
 
 TRUE
 
 
-msk_met_2021
+nsclc_ctdx_msk_2022
 
 
-mixed
+nsclc
 
 
 hg19
 
 
-35120664
+36357680
 
 
-Nguyen et al. Cell 2022
+Jee et al. Nature Medicine 2022
 
 
 FALSE
@@ -18767,13 +18517,11 @@ 
cBioPortalData() && cBioDataPack()<
 
 
 
-Metastatic Non-Small Cell Lung Cancer (MSK, Nature Medicine 2022)
+Pancreatic Neuroendocrine Tumors (MSK, 2023)
 
 
-Targeted sequencing of ctDNA samples drawn from patients with metastatic
-NSCLC using the Resolution ctDx Lung platform. For more information
-contact 
-or 
+Targeted sequencing of 65 Pancreatic Neuroendocrine tumors/normal pairs
+via MSK-IMPACT.
 
 
 TRUE
@@ -18784,28 +18532,216 @@ 
cBioPortalData() && cBioDataPack()<
 0
 
 
-2023-08-16 22:58:19
+2023-08-21 20:20:39
 
 
-2621
+65
 
 
 TRUE
 
 
-nsclc_ctdx_msk_2022
+panc_msk_2023
 
 
-nsclc
+pancreas
 
 
 hg19
 
 
-36357680
+NA
 
 
-Jee et al. Nature Medicine 2022
+NA
+
+
+NA
+
+
+NA
+
+
+
+
+Endometrial Carcinoma Ancestry (MSK, Cancer Discovery 2023)
+
+
+Targeted sequencing of 1882 Endometrial Cancer tumor and normal pairs
+via MSK-IMPACT.
+
+
+TRUE
+
+
+
+
+0
+
+
+2023-09-01 08:02:50
+
+
+1882
+
+
+TRUE
+
+
+ucec_ancestry_cds_msk_2023
+
+
+ucec
+
+
+hg19
+
+
+NA
+
+
+NA
+
+
+NA
+
+
+NA
+
+
+
+
+Esophageal/Stomach Cancer (MSK, 2023)
+
+
+Targeted sequencing of 902 Esophageal/stomach cancer patients via
+MSK-IMPACT.
+
+
+TRUE
+
+
+
+
+0
+
+
+2023-09-05 16:02:41
+
+
+902
+
+
+TRUE
+
+
+egc_msk_2023
+
+
+stomach
+
+
+hg19
+
+
+NA
+
+
+NA
+
+
+NA
+
+
+NA
+
+
+
+
+MSK-IMPACT Heme Tumors (MSK, 2022)
+
+
+Targeted sequencing of 2383 myeloid and lymphoid neoplasms and their
+matched normals via MSK-IMPACT Heme panel.
+
+
+TRUE
+
+
+
+
+0
+
+
+2023-09-08 16:02:51
+
+
+2383
+
+
+TRUE
+
+
+heme_msk_impact_2022
+
+
+mixed
+
+
+hg19
+
+
+NA
+
+
+NA
+
+
+NA
+
+
+NA
+
+
+
+
+Urothelial Carcinoma (BCAN/HCRN, Nat Commun 2022)
+
+
+UC-GENOME: Urothelial Cancer-GENOmic analysis to iMprove patient
+outcomes and rEsearch.
+
+
+TRUE
+
+
+
+
+0
+
+
+2023-10-10 16:25:54
+
+
+192
+
+
+TRUE
+
+
+blca_bcan_hcrn_2022
+
+
+blca
+
+
+hg19
+
+
+36333289
+
+
+Damrauer et al. Nat Commun. 2022
 
 
 FALSE
@@ -18816,7 +18752,7 @@ 
cBioPortalData() && cBioDataPack()<
 
 
 
-Sequential Rhabdomyosarcomas (MSK, Nature Precision Oncology 2023)
+Sequential Rhabdomyosarcomas (MSK, NPJ Precis Oncol 2023)
 
 
 Targeted sequencing of 42 rhabdomyosarcoma tumors and their matched
@@ -18831,7 +18767,7 @@ 
cBioPortalData() && cBioDataPack()<
 0
 
 
-2023-08-21 20:18:46
+2023-10-10 16:56:24
 
 
 42
@@ -18849,10 +18785,10 @@ 
cBioPortalData() && cBioDataPack()<
 hg19
 
 
-NA
+37730754
 
 
-NA
+Wardin et at. NPJ Precis Oncol. 2023
 
 
 NA
@@ -18863,11 +18799,12 @@ 
cBioPortalData() && cBioDataPack()<
 
 
 
-Pancreatic Neuroendocrine Tumors (MSK, 2023)
+Diffuse Glioma (MSK, 2023)
 
 
-Targeted sequencing of 65 Pancreatic Neuroendocrine tumors/normal pairs
-via MSK-IMPACT.
+Targeted sequencing of 73 diffuse gliomas and their matched normal pairs
+via MSK-IMPACT platforms. The data is available on
+Synapse.
 
 
 TRUE
@@ -18878,19 +18815,19 @@ 
cBioPortalData() && cBioDataPack()<
 0
 
 
-2023-08-21 20:20:39
+2023-10-17 08:23:16
 
 
-65
+73
 
 
 TRUE
 
 
-panc_msk_2023
+difg_msk_2023
 
 
-pancreas
+difg
 
 
 hg19
@@ -18910,11 +18847,164 @@ 
cBioPortalData() && cBioDataPack()<
 
 
 
+MSK MetTropism (MSK, Cell 2021)
+
+
+MSK-MET (Memorial Sloan Kettering - Metastatic Events and Tropisms) is
+an integrated pan-cancer cohort of tumor genomic and clinical outcome
+data from 25,000 patients. We analyzed this dataset to identify
+associations between tumor genomic alterations and patterns of
+metastatic dissemination across 50 tumor types. We found that
+chromosomal instability is strongly correlated with metastatic burden in
+some tumor types, including prostate adenocarcinoma, lung adenocarcinoma
+and HR+/HER2+ breast ductal carcinoma, but not in others, such as
+colorectal MSS, pancreatic adenocarcinoma and high-grade serous ovarian
+cancer. We also identified specific somatic alterations associated with
+increased metastatic burden and specific routes of metastatic spread.
+Our data offer a unique resource for the investigation of the biologic
+basis for metastatic spread and highlight the crucial role of
+chromosomal instability in cancer progression
+
+
+TRUE
+
+
+
+
+0
+
+
+2023-10-20 08:24:52
+
+
+25775
+
+
+TRUE
+
+
+msk_met_2021
+
+
+mixed
+
+
+hg19
+
+
+35120664
+
+
+Nguyen et al. Cell 2022
+
+
+FALSE
+
+
+TRUE
+
+
+
+
+Cervical Cancer (MSK, Clin Cancer Res 2023)
+
+
+Targeted Sequencing of 177 cervical tumors and their matched normal
+samples via MSK-IMPACT.
+
+
+TRUE
+
+
+
+
+0
+
+
+2023-10-25 08:26:25
+
+
+177
+
+
+TRUE
+
+
+cervix_msk_2023
+
+
+cervix
+
+
+hg19
+
+
+37643132
+
+
+Friedman et al. Clin Cancer Res 2023
+
+
+NA
+
+
+NA
+
+
+
+
+Mature T and NK Neoplasms (MSK, Blood Adv 2023)
+
+
+Targeted sequencing of 132 Mature T and NK Neoplasms and their matched
+normals via MSK-IMPACT.
+
+
+TRUE
+
+
+
+
+0
+
+
+2023-10-25 17:28:44
+
+
+132
+
+
+TRUE
+
+
+mtnn_msk_2022
+
+
+mtnn
+
+
+hg19
+
+
+37078708
+
+
+William T et al. Blood Adv 2023
+
+
+FALSE
+
+
+FALSE
+
+
+
+
 Bladder Cancer (MSK, Clin Cancer Research 2023)
 
 
 Targeted Sequencing of 526 bladder tumors and their matched normals via
-MSK-IMPACT
+MSK-IMPACT.
 
 
 TRUE
@@ -18925,7 +19015,7 @@ 
cBioPortalData() && cBioDataPack()<
 0
 
 
-2023-08-24 08:02:48
+2023-10-25 17:55:22
 
 
 526
@@ -18943,10 +19033,10 @@ 
cBioPortalData() && cBioDataPack()<
 hg19
 
 
-NA
+37682528
 
 
-NA
+Guercio et al. Clin Cancer Res. 2023
 
 
 NA
@@ -18957,58 +19047,59 @@ 
cBioPortalData() && cBioDataPack()<
 
 
 
-Endometrial Carcinoma Ancestry (MSK, Cancer Discovery 2023)
+Non-Small Cell Lung Cancer (MSK, Science 2015)
 
 
-Targeted sequencing of 1882 Endometrial Cancer tumor and normal pairs
-via MSK-IMPACT.
+Whole-exome sequencing of tumor-normal tissue pairs from 16 non-small
+cell lung cancer samples.
 
 
 TRUE
 
 
+PUBLIC
 
 
 0
 
 
-2023-09-01 08:02:50
+2023-10-27 19:55:27
 
 
-1882
+16
 
 
 TRUE
 
 
-ucec_ancestry_cds_msk_2023
+nsclc_mskcc_2015
 
 
-ucec
+nsclc
 
 
 hg19
 
 
-NA
+25765070
 
 
-NA
+Rivzi et al. Science 2016
 
 
-NA
+TRUE
 
 
-NA
+TRUE
 
 
 
 
-Esophageal/Stomach Cancer (MSK, 2023)
+Pancreatic Neuroendocrine Tumors (MSK, 2023)
 
 
-Targeted sequencing of 902 Esophageal/stomach cancer patients via
-MSK-IMPACT.
+Targeted sequencing of 65 Pancreatic Neuroendocrine tumors/normal pairs
+via MSK-IMPACT.
 
 
 TRUE
@@ -19019,19 +19110,19 @@ 
cBioPortalData() && cBioDataPack()<
 0
 
 
-2023-09-05 16:02:41
+2023-10-31 08:25:43
 
 
-902
+65
 
 
 TRUE
 
 
-egc_msk_2023
+panet_msk_erc_2023
 
 
-stomach
+pancreas
 
 
 hg19
@@ -19051,34 +19142,36 @@ 
cBioPortalData() && cBioDataPack()<
 
 
 
-MSK-IMPACT Heme Tumors (MSK, 2022)
+Breast Invasive Carcinoma (TCGA, Firehose Legacy)
 
 
-Targeted sequencing of 2383 myeloid and lymphoid neoplasms and their
-matched normals via MSK-IMPACT Heme panel.
+TCGA Breast Invasive Carcinoma. Source data from
+GDAC
+Firehose. Previously known as TCGA Provisional.
 
 
 TRUE
 
 
+PUBLIC
 
 
 0
 
 
-2023-09-08 16:02:51
+2023-11-09 17:45:45
 
 
-2383
+1108
 
 
 TRUE
 
 
-heme_msk_impact_2022
+brca_tcga
 
 
-mixed
+brca
 
 
 hg19
@@ -19090,10 +19183,10 @@ 
cBioPortalData() && cBioDataPack()<
 NA
 
 
-NA
+TRUE
 
 
-NA
+TRUE
 
 
 
@@ -19112,7 +19205,7 @@ 
cBioPortalData() && cBioDataPack()<
 0
 
 
-2023-09-23 08:22:12
+2023-11-14 17:23:37
 
 
 322
diff --git a/authors.html b/authors.html
index fcdda18..5ba2e64 100644
--- a/authors.html
+++ b/authors.html
@@ -97,15 +97,16 @@ 
Citation

 
     
Ramos M, Waldron L (2023).
 MultiAssayWorkshop: Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment.
-https://waldronlab.github.io/MultiAssayWorkshop/,
-docker.io/mr148/multiassayworkshop. 
+R package version 3.18.0, 
+docker.io/mr148/multiassayworkshop, https://waldronlab.github.io/MultiAssayWorkshop/. 
 

     
@Manual{,
   title = {MultiAssayWorkshop: Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment},
   author = {Marcel Ramos and Levi Waldron},
   year = {2023},
-  note = {https://waldronlab.github.io/MultiAssayWorkshop/,
+  note = {R package version 3.18.0, 
 docker.io/mr148/multiassayworkshop},
+  url = {https://waldronlab.github.io/MultiAssayWorkshop/},
 }

 
   
diff --git a/pkgdown.yml b/pkgdown.yml
index fd35e25..d5b0b55 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   TCGAutilsCheatsheet: TCGAutilsCheatsheet.html
   cBioPortal_Studies: cBioPortal_Studies.html
   curatedTCGAData_ref: curatedTCGAData_ref.html
-last_built: 2023-09-26T15:58Z
+last_built: 2023-11-21T17:37Z
 urls:
   reference: https://waldronlab.io/MultiAssayWorkshop/reference
   article: https://waldronlab.io/MultiAssayWorkshop/articles