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gdc
•
reset
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
1.5k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R
gdc
rna-seq
dna methylation
updated 5.4 years ago by
Sean Davis
21k • written 5.4 years ago by
RichardJActon
▴ 50
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
3
votes
2
replies
2.1k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 23 months ago by
cute scientist
• 0 • written 5.4 years ago by
Antonio Ahn
▴ 10
1
vote
2
replies
1.3k
views
TCGA MAF (Mutations) data
TCGA
MAF
GDC
snp
mutations
updated 4.9 years ago by
Sean Davis
21k • written 4.9 years ago by
mario.zanfardino
▴ 160
0
votes
0
replies
954
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks
filtering
gdc
TCGABiolinks
rnaseq
4.2 years ago
jam526
• 0
0
votes
11
replies
3.1k
views
TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks
gdc
7.4 years ago
jshelton
• 0
0
votes
1
reply
466
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA
GenomicDataCommons
GDC
written 9 months ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
2
replies
3.6k
views
Extract gene expression values from GDCprepare object
tcgabiolinks
tcga
tcgadownload
gdcprepare
gdc
updated 7.0 years ago by
Tiago Chedraoui Silva
▴ 260 • written 7.2 years ago by
enigmargs
• 0
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
6.0 years ago
pfrancislyon
• 0
0
votes
4
replies
1.1k
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks
TCGA
GDC
4.3 years ago
modarzi
▴ 10
0
votes
0
replies
690
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks
GDC
TCGA
4.3 years ago
modarzi
▴ 10
12 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
transcript name mapping between human and mouse
transcript name mapping between human and mouse
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
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