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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
1.6k
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
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
3
votes
2
replies
2.1k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 2.0 years 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 5.0 years ago by
Sean Davis
21k • written 5.0 years ago by
mario.zanfardino
▴ 160
0
votes
0
replies
974
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks
filtering
gdc
TCGABiolinks
rnaseq
4.3 years ago
jam526
• 0
0
votes
11
replies
3.2k
views
TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks
gdc
7.5 years ago • updated 7.4 years ago
jshelton
• 0
0
votes
1
reply
497
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA
GenomicDataCommons
GDC
written 10 months ago by
António Miguel de Jesus Domingues
▴ 490
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 7.2 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
6.1 years ago
pfrancislyon
• 0
0
votes
4
replies
1.2k
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks
TCGA
GDC
4.4 years ago
modarzi
▴ 10
0
votes
0
replies
710
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks
GDC
TCGA
4.4 years ago
modarzi
▴ 10
12 results • Page
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Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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