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genomicdatacommons
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Why 3 RNA-seq bams for same sample/aliquot_barcode?
manifest
GDCdownload
GenomicDataCommons
8 months ago • updated 7 months ago
xiaofeiwang198266
• 0
0
votes
1
reply
465
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GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA
GenomicDataCommons
GDC
written 9 months ago by
António Miguel de Jesus Domingues
▴ 490
3
votes
2
replies
1.0k
views
How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA
GenomicDataCommons
updated 2.3 years ago by
Robert Castelo
★ 3.1k • written 2.3 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
2.6 years ago
xiaofeiwang18266
▴ 50
0
votes
1
reply
771
views
Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA
GenomicDataCommons
3.0 years ago
Ezgi
▴ 60
0
votes
4
replies
2.2k
views
extract TCGA barcodes and sample_type information from uuids
GenomicDataCommons
R
updated 2.6 years ago by
xiaofeiwang18266
▴ 50 • written 4.1 years ago by
gv
▴ 40
5
votes
11
replies
3.8k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils
TCGAbiolinks
GenomicDataCommons
updated 4.7 years ago by
Marcel Ramos
690 • written 4.7 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 5.2 years ago by
Sean Davis
21k • written 5.2 years ago by
mk
▴ 20
8 results • Page
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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