Showing : genomicdatacommons • reset
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Why 3 RNA-seq bams for same sample/aliquot_barcode?
manifest GDCdownload GenomicDataCommons
8 months ago xiaofeiwang198266 • 0
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1
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499
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GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 10 months ago by ▴ 490
3
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2
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1.1k
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How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA GenomicDataCommons
updated 2.4 years ago by ★ 3.3k • written 2.4 years ago by ▴ 10
4
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4
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1.2k
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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
2.7 years ago xiaofeiwang18266 ▴ 50
0
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1
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803
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Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA GenomicDataCommons
3.1 years ago Ezgi ▴ 60
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4
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2.2k
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extract TCGA barcodes and sample_type information from uuids
GenomicDataCommons R
updated 2.7 years ago by ▴ 50 • written 4.2 years ago by ▴ 40
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11
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3.9k
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Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils TCGAbiolinks GenomicDataCommons
updated 4.8 years ago by 690 • written 4.8 years ago by ★ 1.5k
4
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2
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1.1k
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GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 5.3 years ago by 21k • written 5.3 years ago by ▴ 20
8 results • Page 1 of 1
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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