Showing : tcgabiolinks • reset
0
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2
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95
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TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
22 days ago H. Z. Amini • 0
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0
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60
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TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks TCGAWorkflowData
23 days ago H. Z. Amini • 0
0
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0
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55
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Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
5 weeks ago rebeliscu • 0
0
votes
3
replies
139
views
discrepancy in number of samples
TCGAquery_recount2 TCGAbiolinks
10 weeks ago • updated 9 weeks ago xiaofeiwang18266 ▴ 20
1
vote
1
reply
141
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks RECOUNT2 DESeq2
updated 10 weeks ago by 33k • written 10 weeks ago by ▴ 20
3
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8
replies
366
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
11 weeks ago • updated 10 weeks ago xiaofeiwang18266 ▴ 20
0
votes
0
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81
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Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
12 weeks ago martin.schaefer • 0
0
votes
1
reply
116
views
library(TCGAbiolinks)
TCGAbiolinks
updated 4 months ago by 3.1k • written 4 months ago by • 0
3
votes
7
replies
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
154
views
TCGAbiolinks connection error for GDCquery
MethylationArray TCGAbiolinks
5 months ago • updated 4 months ago Sophie Marion de Proce • 0
0
votes
1
reply
137
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 6 months ago by 2.7k • written 6 months ago by • 0
0
votes
3
replies
196
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
9 months ago aush ▴ 40
0
votes
5
replies
214
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
replies
223
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 9 months ago by ▴ 260 • written 9 months ago by ▴ 40
4
votes
6
replies
255
views
TCGABiolinks downloaded data do not match GDC portal data
TCGAbiolinks
10 months ago mario.zanfardino ▴ 160
0
votes
4
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197
views
TCGAbiolinks installation error because of R.oo installation error
TCGAbiolinks R.oo
updated 11 months ago by 57k • written 11 months ago by ▴ 10
0
votes
2
replies
541
views
TCGAbiolinks BioMart error
TCGAbiolinks BioMart
updated 11 months ago by 57k • written 11 months ago by ▴ 10
1
vote
3
replies
509
views
"Permission denied" when installing TCGAbiolinks and RTCGAToolbox
installation permission denied RTCGAToolbox TCGAbiolinks
13 months ago julia.tutzauer • 0
0
votes
0
replies
125
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
17 months ago jam526 • 0
0
votes
1
reply
611
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
17 months ago ph.shimaasherif • 0
0
votes
0
replies
247
views
Error in downloading the MAF file for the TARGET data
TCGAbiolinks TARGET MAF
18 months ago ph.shimaasherif • 0
2
votes
4
replies
242
views
Error : Results must have the same dimensions
TCGAbiolinks GDC dataset
18 months ago ph.shimaasherif • 0
0
votes
0
replies
157
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
18 months ago modarzi ▴ 10
0
votes
4
replies
249
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
19 months ago modarzi ▴ 10
1
vote
3
replies
330
views
Missing Clinical LIHC Data
Missing Data TCGAbiolinks Kaplan-Meier LIHC Xenabrowser
19 months ago jam526 • 0
0
votes
0
replies
306
views
GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
20 months ago fawazfebin ▴ 30
0
votes
1
reply
200
views
error reading from connection
TCGAbiolinks
updated 11 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
votes
5
replies
629
views
GDCprepare - error
TCGABiolinks GDCprepare
23 months ago vm • 0
2
votes
2
replies
515
views
TCGAbiolinks GDCprepare error
TCGAbiolinks GDCprepare error
updated 23 months ago by ▴ 150 • written 23 months ago by ▴ 10
1
vote
2
replies
229
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga bisulfite tcgabiolinks
updated 24 months ago by ▴ 260 • written 24 months ago by • 0
0
votes
1
reply
459
views
Downloading HTSeq raw reads with TCGABiolinks
TCGAbiolinks RNASEQ
2.0 years ago sherajilir • 0
2
votes
4
replies
444
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
votes
0
replies
260
views
GDCdownload error on CentOS 6.10 server
TCGAbiolinks
2.2 years ago t.kuilman 170
0
votes
0
replies
382
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
votes
0
replies
258
views
TCGAbiolinks specific mutation query
TCGAbiolinks TCGA Mutation GDCquery rnaseq
2.3 years ago Yonatan Amzaleg • 0
1
vote
3
replies
383
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
541
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
623
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
votes
2
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846
views
Error in print.header("GDCquery: Searching in GDC database", "section") :could not find function "print.header",
tcgabiolinks dplyr DT
2.8 years ago Mithil Gaikwad • 0
0
votes
2
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868
views
GDC server down, try to use this package later
tcgabiolinks
2.8 years ago Mithil Gaikwad • 0
0
votes
0
replies
372
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
replies
618
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
votes
4
replies
840
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks tcga genomicdatacommon
2.8 years ago franceschini.gianmarco • 0
0
votes
0
replies
328
views
How to download TCGA mutation data by TCGAbiolinks for a subset of barcode?
TCGAbiolinks
2.9 years ago • updated 2.8 years ago Talip Zengin ▴ 10
0
votes
2
replies
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
votes
1
reply
309
views
TCGAbiolinks OutPuts (5% Losing Information)
tcgabiolinks
2.9 years ago dydrkq777 • 0
0
votes
0
replies
354
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 ...
Replies
Comment: genomicElementDistribution function not found by Arunima • 0
> Package: ChIPpeakAnno Type: Package Version: 3.0.0 Date: 2014-10-24 License: LGPL LazyLoad: yes I have the following package installed …
Answer: genomicElementDistribution function not found by James W. MacDonald 57k
Have you already loaded the package? Also, this part of the default question ``` # include your problematic code here with any corres…
Comment: deseq2 normalized data with heatmap by Ian ▴ 10
Got it, thank you! I will use vsd and potentially scale from there.
Comment: change text size in plotmd functtion by najib • 0
thank you a lot.
Comment: Import MetaPhlAn3 to Phyloseq by Levi Waldron 1.1k
Hi Saraswati, thanks for your interest in that function. Just to clarify for others, it's not part of the curatedMetagenomicData package or…
Votes
A: Deseq2 use fpkm
Comment: deseq2 normalized data with heatmap
Comment: deseq2 normalized data with heatmap
Comment: change text size in plotmd functtion
Answer: change text size in plotmd functtion
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