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TCGABiolinks
•
reset
0
votes
0
replies
71
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks
Proteomics
GENOMICS
bioinformatics
14 days ago
qiz218591
• 0
0
votes
0
replies
56
views
TCGAbiolinks file.type argument
TCGAbiolinks
17 days ago
Elizabeth
• 0
0
votes
0
replies
118
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
6 weeks ago
JAcky
• 0
0
votes
0
replies
98
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks
TCGAbiolinksGUI.data
SummarizedExperiment
9 weeks ago
syednajeebashraf
• 0
5
votes
4
replies
658
views
HTSeq Counts no longer available
TCGAbiolinks
updated 12 weeks ago by
swbarnes2
★ 1.1k • written 4 months ago by
vm
▴ 30
0
votes
2
replies
192
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
TCGAutils
updated 11 weeks ago by
Marcel Ramos
570 • written 3 months ago by
Emre
• 0
0
votes
2
replies
525
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks
TARGET-AML
updated 3 months ago by
Tiago C. Silva
▴ 220 • written 3 months ago by
Лиза
• 0
0
votes
1
reply
430
views
GDCprepare of STAR - counts
GeneExpression
TCGAbiolinks
updated 3 months ago by
Tiago C. Silva
▴ 220 • written 3 months ago by
mahsa
• 0
3
votes
2
replies
1.1k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 3 months ago by
cute scientist
• 0 • written 3.7 years ago by
Antonio Ahn
▴ 10
2
votes
5
replies
637
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks
TCGA
updated 3 months ago by
biologsr
• 0 • written 23 months ago by
aush
▴ 40
0
votes
0
replies
143
views
GDCquery error when querying mutect2 data
TCGAbiolinks
4 months ago
komal.rathi
▴ 100
0
votes
1
reply
393
views
GDCprepare() - R Session Aborted
TCGAbiolinks
R
GDCprepare()
updated 4 months ago by
Tiago C. Silva
▴ 220 • written 4 months ago by
spyrouglykeria
• 0
6
votes
3
replies
1.1k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 3 months ago by
Nikolas
• 0 • written 4 months ago by
lescano
▴ 10
2
votes
8
replies
1.6k
views
GDCquery_Maf error
TCGAbiolinks
GDCquery_Maf
updated 14 days ago by
1526466763
• 0 • written 4 months ago by
e.iich
• 0
0
votes
0
replies
225
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
7 months ago
constantinosdem
• 0
0
votes
0
replies
214
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq
TCGAbiolinks
TCGAAnalyze_DEA
8 months ago
Gandino
• 0
0
votes
1
reply
520
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
9 months ago
raf4
▴ 20
1
vote
2
replies
336
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks
cnv
9 months ago
raf4
▴ 20
0
votes
1
reply
330
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks
WGCNA
updated 11 months ago by
Michael Love
37k • written 11 months ago by
txtbookir
• 0
0
votes
7
replies
2.2k
views
GDCquery(project = "TCGA-COAD") did not work; but GDCquery(project = "TCGA-READ") workl why???
gdcquery
tcgabiolinks
updated 12 months ago by
Jessica
• 0 • written 4.2 years ago by
hwteng1971
• 0
0
votes
0
replies
175
views
DEGs for legacy and harmonized dataset
#DEGs
#legacydataset
#harmonizeddataset
TCGAbiolinks
updated 12 months ago by
Kevin Blighe
3.6k • written 12 months ago by
Gisele
• 0
0
votes
1
reply
328
views
Help With TCGAbiolinks package
TCGAbiolinks
data
normalize
l
updated 12 months ago by
Kevin Blighe
3.6k • written 12 months ago by
DANIELA
• 0
0
votes
2
replies
399
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
14 months ago
H. Z. Amini
• 0
0
votes
0
replies
620
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks
TCGAWorkflowData
14 months ago
H. Z. Amini
• 0
0
votes
0
replies
246
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA
TCGAbiolinks
15 months ago
rebeliscu
• 0
0
votes
3
replies
358
views
discrepancy in number of samples
TCGAquery_recount2
TCGAbiolinks
16 months ago • updated 15 months ago
xiaofeiwang18266
▴ 40
1
vote
1
reply
571
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks
RECOUNT2
DESeq2
updated 16 months ago by
Michael Love
37k • written 16 months ago by
xiaofeiwang18266
▴ 40
3
votes
8
replies
1.5k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
16 months ago
xiaofeiwang18266
▴ 40
0
votes
0
replies
344
views
Job:
Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks
BiomedicalInformatics
Network
16 months ago
martin.schaefer
• 0
0
votes
1
reply
321
views
library(TCGAbiolinks)
TCGAbiolinks
updated 18 months ago by
Kevin Blighe
3.6k • written 18 months ago by
1664424607
• 0
3
votes
7
replies
3.8k
views
how to add a new column in colData in SummarizedExperiment
summarizedexperiment
tcgabiolinks
written 4.2 years ago by
hwteng1971
• 0
0
votes
1
reply
488
views
TCGAbiolinks connection error for GDCquery
MethylationArray
TCGAbiolinks
19 months ago • updated 18 months ago
Sophie Marion de Proce
• 0
0
votes
1
reply
333
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 20 months ago by
shepherl
3.2k • written 20 months ago by
sbetrosian
• 0
0
votes
5
replies
672
views
TCGA: to extract clinical data from barcode
cancer
TCGAbiolinks
updated 23 months ago by
Kevin Blighe
3.6k • written 23 months ago by
Marie DENIS
▴ 10
0
votes
5
replies
772
views
Retrieve TCGA expression data for a single gene
TCGA
TCGAbiolinks
updated 23 months ago by
Tiago Chedraoui Silva
▴ 260 • written 23 months ago by
aush
▴ 40
4
votes
6
replies
631
views
TCGABiolinks downloaded data do not match GDC portal data
TCGAbiolinks
2.0 years ago
mario.zanfardino
▴ 160
0
votes
5
replies
649
views
TCGAbiolinks installation error because of R.oo installation error
TCGAbiolinks
R.oo
updated 7 months ago by
ersan
• 0 • written 2.0 years ago by
Talip Zengin
▴ 10
0
votes
2
replies
1.0k
views
TCGAbiolinks BioMart error
TCGAbiolinks
BioMart
updated 2.1 years ago by
James W. MacDonald
60k • written 2.1 years ago by
Talip Zengin
▴ 10
1
vote
3
replies
2.2k
views
"Permission denied" when installing TCGAbiolinks and RTCGAToolbox
installation
permission denied
RTCGAToolbox
TCGAbiolinks
2.3 years ago
julia.tutzauer
• 0
0
votes
0
replies
342
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks
filtering
gdc
TCGABiolinks
rnaseq
2.5 years ago
jam526
• 0
0
votes
1
reply
1.5k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks
Methylation
GDC data
Data prepare
2.6 years ago
ph.shimaasherif
• 0
0
votes
0
replies
464
views
Error in downloading the MAF file for the TARGET data
TCGAbiolinks
TARGET
MAF
2.6 years ago
ph.shimaasherif
• 0
2
votes
4
replies
504
views
Error : Results must have the same dimensions
TCGAbiolinks
GDC dataset
2.7 years ago
ph.shimaasherif
• 0
0
votes
0
replies
341
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks
GDC
TCGA
2.7 years ago
modarzi
▴ 10
0
votes
4
replies
515
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks
TCGA
GDC
2.7 years ago
modarzi
▴ 10
1
vote
3
replies
696
views
Missing Clinical LIHC Data
Missing Data
TCGAbiolinks
Kaplan-Meier
LIHC
Xenabrowser
2.7 years ago
jam526
• 0
0
votes
0
replies
607
views
GDCprepare error in TCGAbiolinks
tcgabiolinks
gdcprepare
differential expression
2.8 years ago
fawazfebin
▴ 50
0
votes
1
reply
408
views
error reading from connection
TCGAbiolinks
updated 16 months ago by
Kevin Blighe
3.6k • written 2.8 years ago by
471555750
• 0
5
votes
11
replies
2.0k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils
TCGAbiolinks
GenomicDataCommons
updated 3.1 years ago by
Marcel Ramos
570 • written 3.1 years ago by
Dario Strbenac
★ 1.5k
4
votes
5
replies
1.4k
views
GDCprepare - error
TCGABiolinks
GDCprepare
3.1 years ago
vm
▴ 30
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Comment: Data input for aracne2regulon function in viper package
by
xlal
• 0
You are right!And may be we should check the gene symbols cause when I open the expression matrix in EXCEL,it will change some genes into m…
Comment: unable to install.packages("spatialLIBD")
by
Leonardo Collado Torres
▴ 1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment
by
Martin Morgan
25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Delta._.43
▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Alejandro Reyes
★ 1.8k
Thanks for your detail post. I think this might be related to this issue here: https://support.bioconductor.org/p/9143537/ Just to verify…
Votes
Answer: spot- vs cell-level data access
Answer: unable to install.packages("spatialLIBD")
Comment: unable to install.packages("spatialLIBD")
error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
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