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GenomicDataCommons
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Why 3 RNA-seq bams for same sample/aliquot_barcode?
manifest
GDCdownload
GenomicDataCommons
9 months ago
xiaofeiwang198266
• 0
0
votes
1
reply
511
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA
GenomicDataCommons
GDC
written 10 months ago by
António Miguel de Jesus Domingues
▴ 510
3
votes
2
replies
1.1k
views
How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA
GenomicDataCommons
updated 2.4 years ago by
Robert Castelo
★ 3.3k • written 2.4 years ago by
Hashirama
▴ 10
0
votes
4
replies
2.2k
views
extract TCGA barcodes and sample_type information from uuids
GenomicDataCommons
R
updated 2.7 years ago by
xiaofeiwang18266
▴ 50 • written 4.2 years ago by
gv
▴ 40
4
votes
4
replies
1.3k
views
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
votes
1
reply
820
views
Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA
GenomicDataCommons
3.1 years ago
Ezgi
▴ 60
5
votes
11
replies
3.9k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils
TCGAbiolinks
GenomicDataCommons
updated 4.8 years ago by
Marcel Ramos
690 • written 4.8 years ago by
Dario Strbenac
★ 1.5k
4
votes
2
replies
1.1k
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons
tcga
gdc
rest
http
updated 5.3 years ago by
Sean Davis
21k • written 5.3 years ago by
mk
▴ 20
8 results • Page
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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priyanka.m
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