Showing : TCGABiolinks • reset
0
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3.0k
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TCGAbiolinks connection error for GDCquery
MethylationArray TCGAbiolinks
5.0 years ago • updated 4.9 years ago Sophie Marion de Proce • 0
0
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1
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1.4k
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 5.1 years ago by 4.3k • written 5.1 years ago by • 0
0
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5
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4.8k
views
TCGA: to extract clinical data from barcode
cancer TCGAbiolinks
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 10
0
votes
5
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5.6k
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 5.4 years ago by ▴ 260 • written 5.4 years ago by ▴ 40
4
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6
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2.7k
views
TCGABiolinks downloaded data do not match GDC portal data
TCGAbiolinks
5.4 years ago mario.zanfardino ▴ 160
0
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5
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2.4k
views
TCGAbiolinks installation error because of R.oo installation error
TCGAbiolinks R.oo
updated 4.0 years ago by • 0 • written 5.5 years ago by ▴ 10
0
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2
replies
1.8k
views
TCGAbiolinks BioMart error
TCGAbiolinks BioMart
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 10
1
vote
3
replies
5.7k
views
"Permission denied" when installing TCGAbiolinks and RTCGAToolbox
installation permission denied RTCGAToolbox TCGAbiolinks
5.7 years ago julia.tutzauer • 0
0
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0
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1.7k
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Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
6.0 years ago jam526 • 0
0
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1
reply
3.7k
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
6.0 years ago ph.shimaasherif • 0
0
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0
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1.3k
views
Error in downloading the MAF file for the TARGET data
TCGAbiolinks TARGET MAF
6.1 years ago ph.shimaasherif • 0
2
votes
4
replies
1.6k
views
Error : Results must have the same dimensions
TCGAbiolinks GDC dataset
6.1 years ago ph.shimaasherif • 0
0
votes
0
replies
1.1k
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
6.1 years ago modarzi ▴ 10
0
votes
4
replies
2.0k
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
6.1 years ago modarzi ▴ 10
1
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3
replies
2.8k
views
Missing Clinical LIHC Data
Missing Data TCGAbiolinks Kaplan-Meier LIHC Xenabrowser
6.2 years ago jam526 • 0
0
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0
replies
2.1k
views
GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
6.2 years ago fawazfebin ▴ 60
0
votes
1
reply
1.1k
views
error reading from connection
TCGAbiolinks
updated 4.8 years ago by ★ 4.0k • written 6.3 years ago by • 0
5
votes
11
replies
5.8k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils TCGAbiolinks GenomicDataCommons
updated 6.5 years ago by 700 • written 6.5 years ago by ★ 1.6k
4
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5
replies
3.5k
views
GDCprepare - error
TCGABiolinks GDCprepare
6.5 years ago vm ▴ 30
2
votes
2
replies
2.1k
views
TCGAbiolinks GDCprepare error
TCGAbiolinks GDCprepare error
updated 6.5 years ago by ▴ 270 • written 6.5 years ago by ▴ 10
1
vote
2
replies
1.8k
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga bisulfite tcgabiolinks
updated 6.5 years ago by ▴ 260 • written 6.5 years ago by • 0
0
votes
1
reply
2.3k
views
Downloading HTSeq raw reads with TCGABiolinks
TCGAbiolinks RNASEQ
6.6 years ago sherajilir • 0
2
votes
4
replies
2.2k
views
Missing clinical data at TCGAbiolinks data
TCGAbiolinks days_to_death clinical data missing column
updated 6.7 years ago by ▴ 260 • written 6.7 years ago by ▴ 10
0
votes
0
replies
991
views
GDCdownload error on CentOS 6.10 server
TCGAbiolinks
6.7 years ago t.kuilman ▴ 170
0
votes
0
replies
1.7k
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
6.8 years ago gerald.mccollam • 0
0
votes
0
replies
1.5k
views
TCGAbiolinks specific mutation query
TCGAbiolinks TCGA Mutation GDCquery rnaseq
6.8 years ago Yonatan Amzaleg • 0
1
vote
3
replies
3.7k
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks TCGA Download
updated 6.9 years ago by ▴ 260 • written 6.9 years ago by ▴ 10
2
votes
5
replies
5.4k
views
GDCdownload does not work
GDCdow tcgabiolinks error tcgadownload download_error
updated 7.1 years ago by ▴ 260 • written 7.1 years ago by • 0
0
votes
2
replies
2.9k
views
GDCprepare stop working for some unknown reason
tcgabiolinks gdcprepare
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
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2
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2.5k
views
Error in print.header("GDCquery: Searching in GDC database", "section") :could not find function "print.header",
tcgabiolinks dplyr DT
7.3 years ago Mithil Gaikwad • 0
0
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2
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1.9k
views
GDC server down, try to use this package later
tcgabiolinks
7.3 years ago Mithil Gaikwad • 0
0
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0
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1.1k
views
Error while using TCGAanalyze_DMR for >2 groups
methylation tcgabiolinks R gleason score TCGAanalyze_DMR
7.3 years ago mtkk94 • 0
2
votes
5
replies
1.8k
views
TCGAbiolinksGUI is not stable on windows 7.
tcgabiolinks tcgabiolinksgui
updated 7.4 years ago by ▴ 10 • written 7.4 years ago by • 0
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
7.4 years ago ansari.sarabio • 0
3
votes
4
replies
3.6k
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks tcga genomicdatacommon
7.4 years ago gamma.jian ▴ 10
0
votes
0
replies
2.2k
views
How to download TCGA mutation data by TCGAbiolinks for a subset of barcode?
TCGAbiolinks
7.4 years ago Talip ▴ 10
0
votes
2
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3.3k
views
Error: vector memory exhausted (limit reached?)
tcgabiolinks tcga cnv mac os x gaia
updated 7.5 years ago by ▴ 20 • written 7.5 years ago by ▴ 30
0
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1
reply
958
views
TCGAbiolinks OutPuts (5% Losing Information)
tcgabiolinks
7.5 years ago dydrkq777 • 0
0
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0
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1.4k
views
Noise Analyses of CNV Data from TCGA
tcgabiolinks tcga cnv noise pruning
7.5 years ago jrlarsen ▴ 10
1
vote
2
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1.9k
views
Problem for downloading data from Genomic Data Commons portal via TCGAbiolinks package
TCGAbiolinks RNA-seq
7.5 years ago modarzi ▴ 10
2
votes
3
replies
2.6k
views
TCGAbiolinks gives error when parsing a txt file (instead of expected xml)
tcgabiolinks
7.6 years ago andre.verissimo • 0
6
votes
7
replies
3.6k
views
Differences between RTCGA and TCGAbiolinks data
r survival analysis rtcga tcgabiolinks mirna-seq
7.6 years ago atakanekiz ▴ 30
2
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1
reply
2.7k
views
Error in TCGAquery of TCGAbiolinks Package
software error bioconductor tcgabiolinks tcga r
updated 7.6 years ago by ▴ 90 • written 7.6 years ago by ▴ 60
1
vote
6
replies
2.4k
views
Error downloading TCGA miRNA expression data
tcgabiolinks
updated 7.7 years ago by ★ 1.1k • written 7.7 years ago by • 0
3
votes
3
replies
2.2k
views
Retrieve accurate tumor stage data with TCGAbiolinks
tcgabiolinks tcga
7.7 years ago Benjamin Ostendorf ▴ 90
0
votes
1
reply
1.1k
views
TCGAbiolinksGUI(run=TRUE) hangs on Windows 7
tcgabiolinks tcgabiolinksgui
updated 7.8 years ago by ▴ 260 • written 7.8 years ago by • 0
0
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1
reply
4.3k
views
how to infer missing PAM50 molecular subtypes in TCGA-BRCA dataset downloaded with TCGABiolinks?
tcgabiolinks tcga-brca gdc pam50 rna-seq
7.8 years ago pfrancislyon • 0
0
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0
replies
952
views
Problem in using TCGAvisualize_meanMethylation() function?
tcgabiolinks
7.9 years ago mahmood.amiri225 • 0
0
votes
0
replies
1.5k
views
How to get disease free survival information from TCGA using TCGAbiolinks?
tcgabiolinks tcga
7.9 years ago Frocha ▴ 20
2
votes
1
reply
5.6k
views
Using DESeq2 to analyse TCGA data
deseq2 tcga tcgabiolinks gene expression differential expression
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
166 results • Page 2 of 4
Recent ...
Replies
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, Gender is more a nuisance factor in our experiment, and our primary interest is to compare groups. I will just use filter…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Votes
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
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Autobiographer to Frances Turner ▴ 20
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Commentator to James W. MacDonald 68k
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