Showing : TCGAbiolinks • reset
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TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
15 days ago H. Z. Amini • 0
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50
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TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks TCGAWorkflowData
16 days ago H. Z. Amini • 0
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0
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52
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Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
4 weeks ago rebeliscu • 0
0
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3
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137
views
discrepancy in number of samples
TCGAquery_recount2 TCGAbiolinks
9 weeks ago • updated 8 weeks ago xiaofeiwang18266 ▴ 20
1
vote
1
reply
131
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks RECOUNT2 DESeq2
updated 9 weeks ago by 33k • written 9 weeks ago by ▴ 20
3
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8
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355
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
10 weeks ago • updated 9 weeks ago xiaofeiwang18266 ▴ 20
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0
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73
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Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
11 weeks ago martin.schaefer • 0
0
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1
reply
115
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library(TCGAbiolinks)
TCGAbiolinks
updated 4 months ago by 3.1k • written 4 months ago by • 0
3
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7
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2.2k
views
how to add a new column in colData in SummarizedExperiment
summarizedexperiment tcgabiolinks
written 3.0 years ago by • 0
0
votes
1
reply
151
views
TCGAbiolinks connection error for GDCquery
MethylationArray TCGAbiolinks
5 months ago • updated 4 months ago Sophie Marion de Proce • 0
0
votes
1
reply
135
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 6 months ago by 2.7k • written 6 months ago by • 0
0
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3
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190
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
9 months ago aush ▴ 40
0
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5
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206
views
TCGA: to extract clinical data from barcode
cancer TCGAbiolinks
updated 9 months ago by 3.1k • written 9 months ago by ▴ 10
0
votes
5
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218
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Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 9 months ago by ▴ 260 • written 9 months ago by ▴ 40
4
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6
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253
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TCGABiolinks downloaded data do not match GDC portal data
TCGAbiolinks
10 months ago mario.zanfardino ▴ 160
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4
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193
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TCGAbiolinks installation error because of R.oo installation error
TCGAbiolinks R.oo
updated 10 months ago by 57k • written 10 months ago by ▴ 10
0
votes
2
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524
views
TCGAbiolinks BioMart error
TCGAbiolinks BioMart
updated 11 months ago by 57k • written 11 months ago by ▴ 10
1
vote
3
replies
494
views
"Permission denied" when installing TCGAbiolinks and RTCGAToolbox
installation permission denied RTCGAToolbox TCGAbiolinks
13 months ago julia.tutzauer • 0
0
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0
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120
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
17 months ago jam526 • 0
0
votes
1
reply
598
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r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
17 months ago ph.shimaasherif • 0
0
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0
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245
views
Error in downloading the MAF file for the TARGET data
TCGAbiolinks TARGET MAF
18 months ago ph.shimaasherif • 0
2
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4
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236
views
Error : Results must have the same dimensions
TCGAbiolinks GDC dataset
18 months ago ph.shimaasherif • 0
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0
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152
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
18 months ago modarzi ▴ 10
0
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4
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242
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
18 months ago modarzi ▴ 10
1
vote
3
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326
views
Missing Clinical LIHC Data
Missing Data TCGAbiolinks Kaplan-Meier LIHC Xenabrowser
19 months ago jam526 • 0
0
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0
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303
views
GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
20 months ago fawazfebin ▴ 30
0
votes
1
reply
194
views
error reading from connection
TCGAbiolinks
updated 10 weeks ago by 3.1k • written 20 months ago by • 0
5
votes
11
replies
1.1k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils TCGAbiolinks GenomicDataCommons
updated 23 months ago by 540 • written 23 months ago by ★ 1.5k
4
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5
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615
views
GDCprepare - error
TCGABiolinks GDCprepare
23 months ago vm • 0
2
votes
2
replies
511
views
TCGAbiolinks GDCprepare error
TCGAbiolinks GDCprepare error
updated 23 months ago by ▴ 150 • written 23 months ago by ▴ 10
1
vote
2
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225
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga bisulfite tcgabiolinks
updated 23 months ago by ▴ 260 • written 23 months ago by • 0
0
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1
reply
449
views
Downloading HTSeq raw reads with TCGABiolinks
TCGAbiolinks RNASEQ
24 months ago sherajilir • 0
2
votes
4
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436
views
Missing clinical data at TCGAbiolinks data
TCGAbiolinks days_to_death clinical data missing column
updated 2.2 years ago by ▴ 260 • written 2.2 years ago by ▴ 10
0
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0
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257
views
GDCdownload error on CentOS 6.10 server
TCGAbiolinks
2.2 years ago t.kuilman 170
0
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0
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377
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
2.2 years ago gerald.mccollam • 0
0
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0
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255
views
TCGAbiolinks specific mutation query
TCGAbiolinks TCGA Mutation GDCquery rnaseq
2.2 years ago Yonatan Amzaleg • 0
1
vote
3
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378
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks TCGA Download
updated 2.3 years ago by ▴ 260 • written 2.3 years ago by ▴ 10
2
votes
5
replies
1.1k
views
GDCdownload does not work
GDCdow tcgabiolinks error tcgadownload download_error
updated 2.5 years ago by ▴ 260 • written 2.5 years ago by • 0
0
votes
2
replies
537
views
GDCprepare stop working for some unknown reason
tcgabiolinks gdcprepare
updated 2.5 years ago by 57k • written 2.5 years ago by • 0
3
votes
1
reply
618
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.6 years ago by ★ 1.5k • written 2.6 years ago by ▴ 10
0
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2
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841
views
Error in print.header("GDCquery: Searching in GDC database", "section") :could not find function "print.header",
tcgabiolinks dplyr DT
2.7 years ago Mithil Gaikwad • 0
0
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2
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866
views
GDC server down, try to use this package later
tcgabiolinks
2.7 years ago Mithil Gaikwad • 0
0
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0
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368
views
Error while using TCGAanalyze_DMR for >2 groups
methylation tcgabiolinks R gleason score TCGAanalyze_DMR
2.8 years ago mtkk94 • 0
2
votes
5
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609
views
TCGAbiolinksGUI is not stable on windows 7.
tcgabiolinks tcgabiolinksgui
updated 2.8 years ago by ▴ 10 • written 2.8 years ago by • 0
4
votes
1
reply
12k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R deseq tcgabiolinks
2.8 years ago ansari.sarabio • 0
3
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4
replies
831
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks tcga genomicdatacommon
2.8 years ago franceschini.gianmarco • 0
0
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0
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324
views
How to download TCGA mutation data by TCGAbiolinks for a subset of barcode?
TCGAbiolinks
2.8 years ago Talip Zengin ▴ 10
0
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2
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1.5k
views
Error: vector memory exhausted (limit reached?)
tcgabiolinks tcga cnv mac os x gaia
updated 2.9 years ago by ▴ 20 • written 2.9 years ago by ▴ 20
0
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1
reply
305
views
TCGAbiolinks OutPuts (5% Losing Information)
tcgabiolinks
2.9 years ago dydrkq777 • 0
0
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0
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348
views
Noise Analyses of CNV Data from TCGA
tcgabiolinks tcga cnv noise pruning
3.0 years ago jrlarsen ▴ 10
50 results • Page 1 of 1
Recent ...
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Comment: Data input for aracne2regulon function in viper package by Luna_P • 0
Hello Keith, I am currently trying to use my ARACNE-AP generated networks in Viper. I did all three steps you mentioned above but my prob…
Answer: DESeq2 for allele-specific expression with contrasts between conditions by Michael Love 33k
There is a section in the vignette on interactions that will help you here. You want to test for within-individual effects (`allele`) and c…
Answer: Issues with Tximport by Michael Love 33k
Your file has no version numbers, while your `tx2gene` does have version numbers. While the names look similar, they are not a match. tximp…
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w by Michael Love 33k
This is fine and ignorable, it is coming from upstream packages: our use of a TxDb object to pull out transcript to gene mappings.
Comment: DESeq2: NA's in mcols(object)$betaConv by Michael Love 33k
They are actually rounded to zero in the `dds` which requires integer values.
Votes
Comment: DESeq2: NA's in mcols(object)$betaConv
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w
simultaneous use of robust and weighting methods in limma
simultaneous use of robust and weighting methods in limma
Answer: RUVSeq and Salmon
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