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GDCprepare
•
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0
votes
8
replies
3.0k
views
TCGAbiolinks GDCprepare fails to connect to Biomart web server
tcgabiolinks
gdcprepare
8.1 years ago
sabarinath.chandrasekharan
▴ 10
0
votes
2
replies
4.0k
views
Extract gene expression values from GDCprepare object
tcgabiolinks
tcga
tcgadownload
gdcprepare
gdc
updated 7.6 years ago by
Tiago Chedraoui Silva
▴ 260 • written 7.8 years ago by
enigmargs
• 0
2
votes
2
replies
1.7k
views
TCGAbiolinks GDCprepare error
TCGAbiolinks
GDCprepare
error
updated 5.3 years ago by
Tiago C. Silva
▴ 270 • written 5.3 years ago by
Talip Zengin
▴ 10
0
votes
3
replies
1.5k
views
TCGA controlled data
R
tcgabiolinks
gdcprepare
7.5 years ago
ugandhar.ch1
• 0
0
votes
1
reply
1.8k
views
How to get treatment information with TCGAbiolinks?
gdcprepare
tcgabiolinks
treatment_type
R
data extraction
updated 7.4 years ago by
Dario Strbenac
★ 1.5k • written 7.4 years ago by
newbie
• 0
0
votes
1
reply
1.3k
views
Error during GDCprepare
tcgabiolinks
gdcprepare
updated 8.2 years ago by
Tiago C. Silva
▴ 270 • written 8.2 years ago by
Mariana Boroni
▴ 10
1
vote
5
replies
1.8k
views
Issue with TCGAbiolinks package.
TCGA
GDCprepare
5.8 years ago
salvocomplicazioni1
• 0
0
votes
2
replies
2.1k
views
GDCprepare stop working for some unknown reason
tcgabiolinks
gdcprepare
updated 5.9 years ago by
James W. MacDonald
67k • written 5.9 years ago by
ansari.sarabio
• 0
0
votes
0
replies
975
views
Error in GDCDownload and GDCPrepare for TCGA-PAAD Dataset
GDCPrepare
GDCDownload
2.2 years ago
Manav
• 0
0
votes
0
replies
976
views
Reasoning for illegal operation
tcgabiolinks
illegaloperation
gdcprepare
6.9 years ago
lisa8191
• 0
4
votes
5
replies
2.9k
views
GDCprepare - error
TCGABiolinks
GDCprepare
5.3 years ago
vm
▴ 30
0
votes
0
replies
1.6k
views
GDCprepare error in TCGAbiolinks
tcgabiolinks
gdcprepare
differential expression
5.1 years ago
fawazfebin
▴ 60
12 results • Page
1 of 1
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Answer: Is it possible to parallelise saveHDF5SummarizedExperiment
by
Hervé Pagès
16k
Hi Stefano, Unfortunately HDF5 doesn't support concurrent writing so parallelising is not an option. A few things that maybe could help: …
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
James W. MacDonald
67k
It's a simple two-liner in [getsrc.sh][1] ``` awk -F'\t' 'BEGIN {OFS=FS} {if($3 != $11 && $11 != "-") $3 = $11; print $0}' gene_info > tmp…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
Guido Hooiveld
★ 4.1k
Thanks for changing this! Just to confirm I understood it correctly: the `Symbol` will (still) be used, and will be replaced by `Symbol fro…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
James W. MacDonald
67k
OK, there are 157 MT genes in maybe 6 species for which the symbols are not correct, and I added code to swap the 'Symbol from nomenclature…
Comment: Tximport with RSEM error
by
Michael Love
42k
Would you post a new issue with example code and maybe what the files look like?
Votes
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
A: GOseq analysis with only upregulated or downregulated genes
A: GOseq analysis with only upregulated or downregulated genes
Answer: Properly constructing a hypergeometric test
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