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Why 3 RNA-seq bams for same sample/aliquot_barcode?
manifest GDCdownload GenomicDataCommons
2.3 years ago xiaofeiwang198266 • 0
0
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1
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967
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GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 2.4 years ago by ▴ 510
3
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2
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1.8k
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How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA GenomicDataCommons
updated 3.9 years ago by ★ 3.4k • written 3.9 years ago by ▴ 10
4
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4
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2.2k
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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
4.2 years ago xiaofeiwang18266 ▴ 60
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1.3k
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Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA GenomicDataCommons
4.6 years ago Ezgi ▴ 60
0
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4
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3.6k
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extract TCGA barcodes and sample_type information from uuids
GenomicDataCommons R
updated 4.2 years ago by ▴ 60 • written 5.7 years ago by ▴ 40
5
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11
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5.6k
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Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils TCGAbiolinks GenomicDataCommons
updated 6.3 years ago by 700 • written 6.3 years ago by ★ 1.6k
4
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2
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1.6k
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GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 6.8 years ago by 21k • written 6.8 years ago by ▴ 20
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Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k
This should now be resolved
Answer: Question about collapsing ASVs by genus level during DESeq2 analysis by Michael Love 43k
I'll just note that microbiome stats folks tend to use other tools than DESeq2. > several ASVs belong to the same genus but are not iden…
Answer: Integration: Paired-end vs healthy single-end from a different source by James W. MacDonald 68k
If by reprocess you mean generate libraries and re-sequence, then that's something you could do. Otherwise the biological and technical dif…
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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