Showing : GenomicDataCommons • reset
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Why 3 RNA-seq bams for same sample/aliquot_barcode?
manifest GDCdownload GenomicDataCommons
19 months ago xiaofeiwang198266 • 0
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807
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GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 20 months ago by ▴ 510
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How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA GenomicDataCommons
updated 3.3 years ago by ★ 3.4k • written 3.3 years ago by ▴ 10
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2 questions: why there is nothing for file_ids? How could I generate a manifest file with filtering of Race and Ethnicity?
GenomicDataCommons
3.6 years ago • updated 3.5 years ago xiaofeiwang18266 ▴ 50
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Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA GenomicDataCommons
4.0 years ago Ezgi ▴ 60
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4
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extract TCGA barcodes and sample_type information from uuids
GenomicDataCommons R
updated 3.5 years ago by ▴ 50 • written 5.1 years ago by ▴ 40
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4.9k
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Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils TCGAbiolinks GenomicDataCommons
updated 5.6 years ago by 700 • written 5.6 years ago by ★ 1.6k
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GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 6.1 years ago by 21k • written 6.1 years ago by ▴ 20
8 results • Page 1 of 1
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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