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GenomicDataCommons
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379
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Why 3 RNA-seq bams for same sample/aliquot_barcode?
manifest
GDCdownload
GenomicDataCommons
8 months ago
xiaofeiwang198266
• 0
0
votes
1
reply
496
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA
GenomicDataCommons
GDC
written 10 months ago by
António Miguel de Jesus Domingues
▴ 490
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
4
votes
4
replies
1.2k
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
797
views
Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA
GenomicDataCommons
3.1 years ago
Ezgi
▴ 60
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
5
votes
11
replies
3.8k
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: Different Shrunk Log2FC according with reference
by
Michael Love
41k
I took a look and the posterior width for these (fairly rare) examples overlaps zero. So the posterior when it disagrees is not narrow. An…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Votes
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
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