ArticlePloS one2014
RTCGAToolbox: a new tool for exporting TCGA Firehose data.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
105 citing papers in PubMed.
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- Integration of Multi-Omics Data for the Classification of Glioma Types and Identification of Novel Biomarkers.Bioinformatics and biology insights · 2024Article
- Low EGFL7 expression is associated with high lymph node spread and invasion of lymphatic vessels in colorectal cancer.Scientific reports · 2023Article
- RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor.Bioinformatics (Oxford, England) · 2023Article
- Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.NPJ precision oncology · 2023Article
- High expression of LOC541471, GDAP1, SOD1, and STK25 is associated with poor overall survival of patients with acute myeloid leukemia.Cancer medicine · 2023Article
- Pan-cancer onco-signatures reveal a novel mitochondrial subtype of luminal breast cancer with specific regulators.Journal of translational medicine · 2023Article
- Identification of lncRNAs associated with uterine corpus endometrial cancer prognosis based on the competing endogenous RNA network.International journal of medical sciences · 2023Article
- Dermokine mutations contribute to epithelial-mesenchymal transition and advanced melanoma through ERK/MAPK pathways.PloS one · 2023Article
- Evaluation and Comparison of Multi-Omics Data Integration Methods for Subtyping of Cutaneous Melanoma.Biomedicines · 2022Article
- Article
45 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
Abstract
BACKGROUND &
objectiveManaging data from large-scale projects (such as The Cancer Genome Atlas (TCGA)) for further analysis is an important and time consuming step for research projects. Several efforts, such as the Firehose project, make TCGA pre-processed data publicly available via web services and data portals, but this information must be managed, downloaded and prepared for subsequent steps. We have developed an open source and extensible R based data client for pre-processed data from the Firehouse, and demonstrate its use with sample case studies. Results show that our RTCGAToolbox can facilitate data management for researchers interested in working with TCGA data. The RTCGAToolbox can also be integrated with other analysis pipelines for further data processing. AVAILABILITY AND IMPLEMENTATION: The RTCGAToolbox is open-source and licensed under the GNU General Public License Version 2.0. All documentation and source code for RTCGAToolbox is freely available at http://mksamur.github.io/RTCGAToolbox/ for Linux and Mac OS X operating systems.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.