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tcgabiolinks
•
reset
4
votes
1
reply
14k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R
deseq
tcgabiolinks
5.7 years ago
ansari.sarabio
• 0
1
vote
3
replies
5.7k
views
package ‘TCGAbiolinks’ is not available (for R version 3.2.0)
software error
TCGAbiolinks
updated 8.3 years ago by
Martin Morgan
25k • written 8.3 years ago by
yizhong2md
• 0
2
votes
8
replies
4.9k
views
GDCquery_Maf error
TCGAbiolinks
GDCquery_Maf
updated 21 months ago by
1526466763
• 0 • written 2.1 years ago by
e.iich
• 0
2
votes
1
reply
4.7k
views
Using DESeq2 to analyse TCGA data
deseq2
tcga
tcgabiolinks
gene expression
differential expression
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
victor.ramos.usp
• 0
3
votes
7
replies
4.3k
views
Getting the metadata for a RNA-seq sample from TCGA when you have the uuid
tcgabiolinks
tcgadownload
updated 7.5 years ago by
Tiago Chedraoui Silva
▴ 260 • written 7.5 years ago by
Leonardo Collado Torres
★ 1.0k
1
vote
3
replies
4.3k
views
"Permission denied" when installing TCGAbiolinks and RTCGAToolbox
installation
permission denied
RTCGAToolbox
TCGAbiolinks
4.0 years ago
julia.tutzauer
• 0
0
votes
3
replies
4.3k
views
Problem in downloading data via TCGAbiolinks
tcgabiolinks
tcgadownload
updated 2.9 years ago by
H. Z. Amini
▴ 10 • written 7.8 years ago by
sabarinath.chandrasekharan
▴ 10
2
votes
22
replies
4.2k
views
Error in 'colnames' while running case 1 of TCGABiolinks
tcgabiolinks
Error in `colnames
8.2 years ago
zeeniajagga
• 0
5
votes
11
replies
3.9k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils
TCGAbiolinks
GenomicDataCommons
updated 4.8 years ago by
Marcel Ramos
690 • written 4.8 years ago by
Dario Strbenac
★ 1.5k
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
2
votes
11
replies
3.7k
views
package or namespace load failed for TCGAbiolinks
tcgabiolinks
updated 6.6 years ago by
wenhuo hu
▴ 200 • written 6.6 years ago by
jason.yijialin
• 0
2
votes
5
replies
3.6k
views
GDCdownload does not work
GDCdow
tcgabiolinks
error
tcgadownload
download_error
updated 5.4 years ago by
Tiago Chedraoui Silva
▴ 260 • written 5.4 years ago by
miki716
• 0
0
votes
2
replies
3.6k
views
Error using TCGAbiolinks "Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column"
TCGA
tcgabiolinks
Error
6.9 years ago
f.geist
▴ 20
3
votes
8
replies
3.5k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
3.1 years ago
xiaofeiwang18266
▴ 50
2
votes
6
replies
3.3k
views
Getting a flat metadata table from the XML files in TCGA: is it feasible?
tcgabiolinks
updated 7.5 years ago by
Tiago Chedraoui Silva
▴ 260 • written 7.5 years ago by
Leonardo Collado Torres
★ 1.0k
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
6
votes
3
replies
3.1k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 2.1 years ago by
Nikolas
• 0 • written 2.1 years ago by
lescano
▴ 10
4
votes
20
replies
3.1k
views
TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid for atomic vectors
tcgabiolinks
updated 7.1 years ago by
Mike Smith
★ 6.5k • written 7.1 years ago by
tangming2005
▴ 190
1
vote
3
replies
3.1k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 6 weeks ago by
snijesh
▴ 20 • written 6.6 years ago by
Ramiro Magno
▴ 100
0
votes
6
replies
3.0k
views
TCGAbiolinks DNA methylation analysis TCGAvisualize_meanMethylation
tcgabiolinks
updated 8.1 years ago by
Tiago C. Silva
▴ 270 • written 8.1 years ago by
maedakus
▴ 10
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
6
votes
11
replies
3.0k
views
Error and weird result of TCGAanalyze_Normalization function using the R package TCGAbiolinks for normalization of raw HTSeq counts
tcgabiolinks
rnaseq
normalization
EDASeq
updated 6.4 years ago by
antonio.colaprico
▴ 50 • written 6.5 years ago by
svlachavas
▴ 830
5
votes
4
replies
2.9k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 23 months ago by
swbarnes2
★ 1.3k • written 2.1 years ago by
vm
▴ 30
0
votes
5
replies
2.8k
views
Retrieve TCGA expression data for a single gene
TCGA
TCGAbiolinks
updated 3.7 years ago by
Tiago Chedraoui Silva
▴ 260 • written 3.7 years ago by
aush
▴ 40
0
votes
1
reply
2.7k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks
Methylation
GDC data
Data prepare
4.3 years ago
ph.shimaasherif
• 0
0
votes
2
replies
2.6k
views
Unable to install TCGAbiolinks
tcgabiolinks
updated 6.6 years ago by
shepherl
3.9k • written 6.6 years ago by
rf
• 0
0
votes
8
replies
2.6k
views
TCGAbiolinks GDCprepare fails to connect to Biomart web server
tcgabiolinks
gdcprepare
7.6 years ago
sabarinath.chandrasekharan
▴ 10
0
votes
2
replies
2.6k
views
Error: vector memory exhausted (limit reached?)
tcgabiolinks
tcga
cnv
mac os x
gaia
updated 5.8 years ago by
rreck
▴ 20 • written 5.8 years ago by
rina
▴ 30
6
votes
7
replies
2.5k
views
Differences between RTCGA and TCGAbiolinks data
r
survival analysis
rtcga
tcgabiolinks
mirna-seq
5.9 years ago
atakanekiz
▴ 30
1
vote
3
replies
2.5k
views
Data download via TCGAbiolinks
tcgabiolinks
updated 7.0 years ago by
ugandhar.ch1
• 0 • written 8.3 years ago by
maedakus
▴ 10
4
votes
5
replies
2.5k
views
GDCprepare - error
TCGABiolinks
GDCprepare
4.8 years ago
vm
▴ 30
1
vote
2
replies
2.4k
views
TCGAbiolinks data download problem
cancer
microarray
bioconductor
tcgabiolinks
8.0 years ago
Fernando
• 0
7
votes
6
replies
2.4k
views
Analysis using TCGAbiolinks
tcgabiolinks
triple negative breast cancer
data sets
updated 6.4 years ago by
antonio.colaprico
▴ 50 • written 6.4 years ago by
fawazfebin
▴ 60
3
votes
4
replies
2.4k
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks
tcga
genomicdatacommon
5.7 years ago
franceschini.gianmarco
• 0
4
votes
2
replies
2.3k
views
TCGA-biolink: GRCH38 RNA-seq, normalized counts matrix, Converting ensemble gene name into common gene name
tcgabiolinks
grch38
annotation
updated 6.5 years ago by
Tiago C. Silva
▴ 270 • written 6.6 years ago by
salvocomplicazioni1
• 0
0
votes
4
replies
2.3k
views
TCGA biolinks data download
tcgabiolinks
updated 7.8 years ago by
Tiago C. Silva
▴ 270 • written 7.8 years ago by
maedakus
▴ 10
6
votes
3
replies
2.2k
views
TCGAbiolinks GDCquery Error: Parsing problems
tcgabiolinks
updated 6.5 years ago by
maysa_taheir
▴ 50 • written 6.5 years ago by
Ramiro Magno
▴ 100
2
votes
2
replies
2.2k
views
TCGAbiolinks Download ERROR
TCGA
tcgabiolinks
download
error
updated 6.5 years ago by
eshelden
▴ 40 • written 6.5 years ago by
Talip Zengin
▴ 10
2
votes
1
reply
2.2k
views
Error in TCGAquery of TCGAbiolinks Package
software error
bioconductor
tcgabiolinks
tcga
r
updated 5.9 years ago by
Benjamin Ostendorf
▴ 90 • written 5.9 years ago by
Beginner
▴ 60
3
votes
2
replies
2.2k
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
0
votes
1
reply
2.1k
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
2.5 years ago
raf4
▴ 20
0
votes
2
replies
2.1k
views
GDCprepare() - R Session Aborted
TCGAbiolinks
R
GDCprepare()
2.1 years ago • updated 19 months ago
spyrouglykeria
• 0
0
votes
2
replies
2.1k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks
TARGET-AML
updated 2.0 years ago by
Tiago C. Silva
▴ 270 • written 2.0 years ago by
Лиза
• 0
0
votes
1
reply
2.1k
views
Missing the package called 'R.oo'. Please help me to fix, thanks.
TCGAbiolinks
updated 8.1 years ago by
phil.chapman
▴ 150 • written 8.1 years ago by
sf.tonny
• 0
0
votes
3
replies
2.1k
views
TCGAbiolinks data download error
tcgabiolinks
8.1 years ago
maedakus
▴ 10
1
vote
3
replies
2.1k
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks
TCGA
Download
updated 5.2 years ago by
Tiago Chedraoui Silva
▴ 260 • written 5.2 years ago by
modarzi
▴ 10
2
votes
6
replies
2.1k
views
Using TCGAbiolinks for exon and oligonucleotide level microarray
tcga
tcgabiolinks
microarray
exons
oligonucleotide
updated 8.0 years ago by
Tiago C. Silva
▴ 270 • written 8.0 years ago by
Fernando
• 0
0
votes
5
replies
2.0k
views
TCGA: to extract clinical data from barcode
cancer
TCGAbiolinks
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
Marie DENIS
▴ 10
1
vote
6
replies
2.0k
views
Errors in TCGAbiolinks
tcgabiolinks
updated 7.7 years ago by
Tiago Chedraoui Silva
▴ 260 • written 7.8 years ago by
sabarinath.chandrasekharan
▴ 10
1
vote
7
replies
2.0k
views
Cannot retrieve projects from TCGA using getGDCprojects function
tcgabiolinks
TCGA
software error
6.4 years ago
jacorvar
▴ 40
50 results • Page
1 of 1
Recent ...
Replies
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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