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gdc
•
reset
0
votes
11
replies
3.2k
views
TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks
gdc
7.5 years ago
jshelton
• 0
17
votes
8
replies
3.1k
views
How to check the read length for all the TCGA data samples in GDC?
gdc
tcga
wes
gdc data
updated 6.0 years ago by
Sean Davis
21k • written 6.0 years ago by
Biologist
▴ 110
7
votes
7
replies
1.6k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R
gdc
rna-seq
dna methylation
updated 5.5 years ago by
Sean Davis
21k • written 5.5 years ago by
RichardJActon
▴ 50
0
votes
4
replies
1.2k
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks
TCGA
GDC
4.4 years ago
modarzi
▴ 10
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
0
votes
2
replies
3.7k
views
Extract gene expression values from GDCprepare object
tcgabiolinks
tcga
tcgadownload
gdcprepare
gdc
updated 7.1 years ago by
Tiago Chedraoui Silva
▴ 260 • written 7.3 years ago by
enigmargs
• 0
3
votes
2
replies
2.1k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 2.1 years ago by
cute scientist
• 0 • written 5.5 years ago by
Antonio Ahn
▴ 10
1
vote
2
replies
1.3k
views
TCGA MAF (Mutations) data
TCGA
MAF
GDC
snp
mutations
updated 5.0 years ago by
Sean Davis
21k • written 5.0 years ago by
mario.zanfardino
▴ 160
0
votes
1
reply
3.0k
views
how to infer missing PAM50 molecular subtypes in TCGA-BRCA dataset downloaded with TCGABiolinks?
tcgabiolinks
tcga-brca
gdc
pam50
rna-seq
6.1 years ago
pfrancislyon
• 0
0
votes
1
reply
507
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA
GenomicDataCommons
GDC
written 10 months ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
0
replies
715
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks
GDC
TCGA
4.4 years ago
modarzi
▴ 10
0
votes
0
replies
983
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks
filtering
gdc
TCGABiolinks
rnaseq
4.3 years ago
jam526
• 0
12 results • Page
1 of 1
Recent ...
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Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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