Introduction | Data access and caching | Load TCGA data | Load datasets based on rules | Cleaning of duplicate samples | Association of CXCL12 expression with overall survival | Batch correction with ComBat | Non-specific probe sets | FULLVcuratedOvarianData | Available Clinical Characteristics | Summarizing the List of ExpressionSets | For non-R users | Session Info | References
Package: curatedOvarianData 1.51.5
Levi Waldron
curatedOvarianData: Clinically Annotated Data for the Ovarian Cancer Transcriptome
Manually curated human ovarian cancer ExpressionSet objects from 30 studies, with uniformly processed expression data and standardized clinical metadata including survival outcomes. Datasets are hosted on Zenodo and downloaded on first use, then cached locally with BiocFileCache. Includes a configurable script for rule-based creation of filtered dataset lists for meta-analysis.
Authors:
curatedOvarianData_1.51.5.tar.gz
curatedOvarianData_1.51.5.zip(r-4.7-any)curatedOvarianData_1.51.5.zip(r-4.6-any)
curatedOvarianData_1.51.5.tgz(r-4.6-any)
curatedOvarianData_1.51.5.tar.gz(r-4.7-any)curatedOvarianData_1.51.5.tar.gz(r-4.6-any)
curatedOvarianData_1.51.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
curatedOvarianData/json (API)
| # Install 'curatedOvarianData' in R: |
| install.packages('curatedOvarianData', repos = c('https://waldronlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/waldronlab/curatedovariandata/issues
Datasets:
- E.MTAB.386_eset - Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer.
- GSE12418_eset - Expression analysis of stage III serous ovarian adenocarcinoma distinguishes a sub-group of survivors.
- GSE12470_eset - Gene expression profiling of advanced-stage serous ovarian cancers distinguishes novel subclasses and implicates ZEB2 in tumor progression and prognosis.
- GSE13876_eset - Survival-related profile, pathways, and transcription factors in ovarian cancer.
- GSE14764_eset - A prognostic gene expression index in ovarian cancer - validation across different independent data sets.
- GSE17260_eset - Gene expression profile for predicting survival in advanced-stage serous ovarian cancer across two independent datasets.
- GSE18520_eset - A gene signature predictive for outcome in advanced ovarian cancer identifies a survival factor: microfibril-associated glycoprotein 2.
- GSE19829.GPL570_eset - Gene expression profile of BRCAness that correlates with responsiveness to chemotherapy and with outcome in patients with epithelial ovarian cancer.
- GSE19829.GPL8300_eset - Gene expression profile of BRCAness that correlates with responsiveness to chemotherapy and with outcome in patients with epithelial ovarian cancer.
- GSE20565_eset - A genomic and transcriptomic approach for a differential diagnosis between primary and secondary ovarian carcinomas in patients with a previous history of breast cancer.
- GSE2109_eset - IGC EXpression Project for Oncology
- GSE26193_eset - MiR-141 and miR-200a act on ovarian tumorigenesis by controlling oxidative stress response.
- GSE26712_eset - A gene signature predicting for survival in suboptimally debulked patients with ovarian cancer.
- GSE30009_eset - Multidrug resistance-linked gene signature predicts overall survival of patients with primary ovarian serous carcinoma.
- GSE30161_eset - Multi-gene expression predictors of single drug responses to adjuvant chemotherapy in ovarian carcinoma: predicting platinum resistance.
- GSE32062.GPL6480_eset - High-risk ovarian cancer based on 126-gene expression signature is uniquely characterized by downregulation of antigen presentation pathway.
- GSE32063_eset - High-risk ovarian cancer based on 126-gene expression signature is uniquely characterized by downregulation of antigen presentation pathway.
- GSE44104_eset - COL11A1 promotes tumor progression and predicts poor clinical outcome in ovarian cancer.
- GSE49997_eset - Validating the impact of a molecular subtype in ovarian cancer on outcomes: a study of the OVCAD Consortium.
- GSE51088_eset - POSTN/TGFBI-associated stromal signature predicts poor prognosis in serous epithelial ovarian cancer.
- GSE6008_eset - Lysophosphatidic acid-induced transcriptional profile represents serous epithelial ovarian carcinoma and worsened prognosis.
- GSE6822_eset - Classification of ovarian tumor samples
- GSE8842_eset - Analysis of gene expression in early-stage ovarian cancer.
- GSE9891_eset - Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome.
- PMID15897565_eset - Patterns of gene expression that characterize long-term survival in advanced stage serous ovarian cancers.
- PMID17290060_eset - An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer.
- PMID19318476_eset - Microarray analysis of early stage serous ovarian cancers shows profiles predictive of favorable outcome.
- TCGA_eset - Integrated genomic analyses of ovarian carcinoma.
- TCGA.mirna.8x15kv2_eset - Integrated genomic analyses of ovarian carcinoma.
- TCGA.RNASeqV2_eset - Integrated genomic analyses of ovarian carcinoma.
On BioConductor:curatedOvarianData-1.51.4(data/experiment 3.24)curatedOvarianData-1.50.0(data/experiment 3.23)
experimentdataexpressiondatacancerdataovariancancerdatamicroarraydatamirnadatarnaseqdataarrayexpressgeobioconductor-packageu24ca289073
Last updated from:9fe9192483. Checks:5 NOTE, 2 OK, 2 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 189 | ||
| source / vignettes | OK | 418 | ||
| linux-release | NOTE | 182 | ||
| macos-release | NOTE | 144 | ||
| macos-oldrel | FAIL | 91 | ||
| windows-devel | NOTE | 129 | ||
| windows-release | NOTE | 120 | ||
| windows-oldrel | FAIL | 60 | ||
| wasm-release | OK | 146 |
Exports:curatedOvarianData
Dependencies:askpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrdplyrfastmapfilelockgenericsgluehttr2lifecyclemagrittrmemoiseopensslpillarpkgconfigpurrrR6rlangRSQLitestringistringrsystibbletidyrtidyselectutf8vctrswithr
