Showing : TCGABiolinks • reset
0
votes
1
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64
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pre-proccessing of TCGA data for WGCNA
TCGAbiolinks WGCNA
updated 28 days ago by 34k • written 29 days ago by • 0
0
votes
7
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1.6k
views
GDCquery(project = "TCGA-COAD") did not work; but GDCquery(project = "TCGA-READ") workl why???
gdcquery tcgabiolinks
updated 5 weeks ago by • 0 • written 3.3 years ago by • 0
0
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0
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61
views
DEGs for legacy and harmonized dataset
#DEGs #legacydataset #harmonizeddataset TCGAbiolinks
updated 6 weeks ago by 3.4k • written 6 weeks ago by • 0
0
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1
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102
views
Help With TCGAbiolinks package
TCGAbiolinks data normalize l
updated 7 weeks ago by 3.4k • written 7 weeks ago by • 0
0
votes
2
replies
161
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
3 months ago H. Z. Amini • 0
0
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0
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148
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks TCGAWorkflowData
3 months ago H. Z. Amini • 0
0
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0
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99
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
4 months ago rebeliscu • 0
0
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3
replies
204
views
discrepancy in number of samples
TCGAquery_recount2 TCGAbiolinks
5 months ago xiaofeiwang18266 ▴ 40
1
vote
1
reply
225
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks RECOUNT2 DESeq2
updated 5 months ago by 34k • written 5 months ago by ▴ 40
3
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8
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607
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
5 months ago xiaofeiwang18266 ▴ 40
0
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0
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155
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
5 months ago martin.schaefer • 0
0
votes
1
reply
166
views
library(TCGAbiolinks)
TCGAbiolinks
updated 7 months ago by 3.4k • written 7 months ago by • 0
3
votes
7
replies
2.5k
views
how to add a new column in colData in SummarizedExperiment
summarizedexperiment tcgabiolinks
written 3.3 years ago by • 0
0
votes
1
reply
205
views
TCGAbiolinks connection error for GDCquery
MethylationArray TCGAbiolinks
8 months ago • updated 7 months ago Sophie Marion de Proce • 0
0
votes
1
reply
180
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 9 months ago by 2.8k • written 9 months ago by • 0
0
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3
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267
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
12 months ago aush ▴ 40
0
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5
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301
views
TCGA: to extract clinical data from barcode
cancer TCGAbiolinks
updated 12 months ago by 3.4k • written 12 months ago by ▴ 10
0
votes
5
replies
290
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 12 months ago by ▴ 260 • written 12 months ago by ▴ 40
4
votes
6
replies
329
views
TCGABiolinks downloaded data do not match GDC portal data
TCGAbiolinks
13 months ago mario.zanfardino ▴ 160
0
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4
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250
views
TCGAbiolinks installation error because of R.oo installation error
TCGAbiolinks R.oo
updated 14 months ago by 58k • written 14 months ago by ▴ 10
0
votes
2
replies
680
views
TCGAbiolinks BioMart error
TCGAbiolinks BioMart
updated 14 months ago by 58k • written 14 months ago by ▴ 10
1
vote
3
replies
724
views
"Permission denied" when installing TCGAbiolinks and RTCGAToolbox
installation permission denied RTCGAToolbox TCGAbiolinks
16 months ago julia.tutzauer • 0
0
votes
0
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172
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
20 months ago jam526 • 0
0
votes
1
reply
787
views
r: vector memory exhausted (limit reached?)
TCGAbiolinks Methylation GDC data Data prepare
20 months ago ph.shimaasherif • 0
0
votes
0
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293
views
Error in downloading the MAF file for the TARGET data
TCGAbiolinks TARGET MAF
21 months ago ph.shimaasherif • 0
2
votes
4
replies
318
views
Error : Results must have the same dimensions
TCGAbiolinks GDC dataset
21 months ago ph.shimaasherif • 0
0
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0
replies
189
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
21 months ago modarzi ▴ 10
0
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4
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314
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
22 months ago modarzi ▴ 10
1
vote
3
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410
views
Missing Clinical LIHC Data
Missing Data TCGAbiolinks Kaplan-Meier LIHC Xenabrowser
22 months ago jam526 • 0
0
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0
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360
views
GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
23 months ago fawazfebin ▴ 30
0
votes
1
reply
257
views
error reading from connection
TCGAbiolinks
updated 5 months ago by 3.4k • written 23 months ago by • 0
5
votes
11
replies
1.3k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils TCGAbiolinks GenomicDataCommons
updated 2.2 years ago by 550 • written 2.2 years ago by ★ 1.5k
4
votes
5
replies
818
views
GDCprepare - error
TCGABiolinks GDCprepare
2.2 years ago vm • 0
2
votes
2
replies
611
views
TCGAbiolinks GDCprepare error
TCGAbiolinks GDCprepare error
updated 2.2 years ago by ▴ 150 • written 2.2 years ago by ▴ 10
1
vote
2
replies
279
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga bisulfite tcgabiolinks
updated 2.2 years ago by ▴ 260 • written 2.2 years ago by • 0
0
votes
1
reply
530
views
Downloading HTSeq raw reads with TCGABiolinks
TCGAbiolinks RNASEQ
2.3 years ago • updated 2.2 years ago sherajilir • 0
2
votes
4
replies
533
views
Missing clinical data at TCGAbiolinks data
TCGAbiolinks days_to_death clinical data missing column
updated 2.4 years ago by ▴ 260 • written 2.4 years ago by ▴ 10
0
votes
0
replies
295
views
GDCdownload error on CentOS 6.10 server
TCGAbiolinks
2.4 years ago t.kuilman 170
0
votes
0
replies
426
views
TCGAanalyze_DMR error when calculating mean methylation difference between two groups.
TCGAbiolinks SummarizedExperiment TCGAanalyze_DMR methylation R
2.5 years ago gerald.mccollam • 0
0
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0
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304
views
TCGAbiolinks specific mutation query
TCGAbiolinks TCGA Mutation GDCquery rnaseq
2.5 years ago Yonatan Amzaleg • 0
1
vote
3
replies
448
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks TCGA Download
updated 2.6 years ago by ▴ 260 • written 2.6 years ago by ▴ 10
2
votes
5
replies
1.2k
views
GDCdownload does not work
GDCdow tcgabiolinks error tcgadownload download_error
updated 2.8 years ago by ▴ 260 • written 2.8 years ago by • 0
0
votes
2
replies
715
views
GDCprepare stop working for some unknown reason
tcgabiolinks gdcprepare
updated 2.8 years ago by 58k • written 2.8 years ago by • 0
3
votes
1
reply
697
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.8 years ago by ★ 1.5k • written 2.8 years ago by ▴ 10
0
votes
2
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929
views
Error in print.header("GDCquery: Searching in GDC database", "section") :could not find function "print.header",
tcgabiolinks dplyr DT
3.0 years ago Mithil Gaikwad • 0
0
votes
2
replies
924
views
GDC server down, try to use this package later
tcgabiolinks
3.0 years ago Mithil Gaikwad • 0
0
votes
0
replies
415
views
Error while using TCGAanalyze_DMR for >2 groups
methylation tcgabiolinks R gleason score TCGAanalyze_DMR
3.0 years ago mtkk94 • 0
2
votes
5
replies
698
views
TCGAbiolinksGUI is not stable on windows 7.
tcgabiolinks tcgabiolinksgui
updated 3.1 years ago by ▴ 10 • written 3.1 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
3.1 years ago ansari.sarabio • 0
3
votes
4
replies
948
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks tcga genomicdatacommon
3.1 years ago franceschini.gianmarco • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: VST transformation and covariates in the TCGA TARGET GTEx dataset by Michael Love 34k
If this is taking too long, you can run it on a subsample (e.g. hundreds of samples) to identify parameters for the VST, and then apply it …
Comment: "full model matrix is less than full rank" by fernandogs97 • 0
Hello ATpoint, thank you very much for your fast and helpful response, finally I corrected the error by changing the separator, instead of …
Comment: unable to load shared object Rsamtools.dll': by Mike Smith ★ 5.1k
Can you include the command you're running (I guess it's `BiocManager::install("Rsamtools", type = "source")` )? It would also be useful to…
Comment: unable to load shared object Rsamtools.dll': by franck.richard • 0
Finally, I only encounter this problem with Rsamtools. It works fine with the other packages. Thank you for your help!
Comment: Unique GPos taking into account mcols by maltethodberg ▴ 140
Yes, I managed to find those functions via the VariantAnnotation package. The "Quad" versions are very handy for matching seqnames/pos/effe…
Votes
Answer: "full model matrix is less than full rank"
Comment: Unique GPos taking into account mcols
Comment: deseq2 machine sizing best practices for very large data set
Comment: Warning messages on Apple M1 BigSur
Answer: VST transformation and covariates in the TCGA TARGET GTEx dataset
Awards • All
Popular Question to Michael Stadler ▴ 340
Scholar to Mike Smith ★ 5.1k
Scholar to Gordon Smyth 43k
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Popular Question to Hans-Ulrich Klein ▴ 330
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