Alternatively processed and compiled RNA-Sequencing and clinical data for thousands of samples from The Cancer Genome Atlas
We reprocessed RNA-Seq data for 9264 tumor samples and 741 normal samples across 24 cancer types from The Cancer Genome Atlas with "Rsubread". Rsubread is an open source R package that has shown high concordance with other existing methods of alignment and summarization, but is simple to use and takes significantly less time to process data. Additionally, we provide clinical variables publicly available as of May 20, 2015 for the tumor samples where the TCGA ids are matched.
Provenance — who produced it, who reused it
Linked to 57 papers in the literature. Roles are inferred factual signals (who deposited the data vs who reused it), with counts — never a judgement about any author.
- Systematic pan-cancer analysis of tumour purity 2015 · 1,301 cites
- Spatially organized multicellular immune hubs in human colorecta... 2021 · 810 cites
- Comprehensive analysis of normal adjacent to tumor transcriptome... 2017 · 647 cites
- The functional landscape of the human phosphoproteome 2019 · 498 cites
- Atlas of clinically distinct cell states and ecosystems across h... 2021 · 341 cites
- Transcription Factor Activities Enhance Markers of Drug Sensitiv... 2017 · 235 cites
- Integration of machine learning and genome-scale metabolic model... 2021 · 191 cites
- FUT8-mediated aberrant N-glycosylation of B7H3 suppresses the im... 2021 · 180 cites
- Widespread Post-transcriptional Attenuation of Genomic Copy-Numb... 2017 · 143 cites
- Portraying breast cancers with long noncoding RNAs 2016 · 116 cites
- Stable gene expression for normalisation and single-sample scori... 2020 · 108 cites
- HOXBLINC long non-coding RNA activation promotes leukemogenesis... 2021 · 96 cites
- Bioconductor’s EnrichmentBrowser: seamless navigation through co... 2016 · 94 cites
- Bacteria-to-Human Protein Networks Reveal Origins of Endogenous... 2019 · 94 cites
- PTEN loss correlates with T cell exclusion across human cancers 2021 · 91 cites
- MYC Dysregulates Mitosis, Revealing Cancer Vulnerabilities 2020 · 81 cites
- Identifying and targeting cancer-specific metabolism with networ... 2019 · 80 cites
- WNT4 mediates estrogen receptor signaling and endocrine resistan... 2016 · 79 cites
- A Peroxidase Peroxiredoxin 1-Specific Redox Regulation of the No... 2017 · 71 cites
37 further papers cite this accession but reuse could not be confirmed.
Deep data QC
metadata only · no data-level QC for this typeStandardized, field-standard QC computed by touching the data — every metric states how it was obtained
measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0 · provisional — verify independently