Showing : TCGAbiolinks • reset
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maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error maftools tcgabiolinks
updated 8 weeks ago by ▴ 20 • written 6.6 years ago by ▴ 100
0
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1
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248
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks TCGA clinical TCGA-BRCA
written 9 weeks ago by • 0
0
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0
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166
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
10 weeks ago • updated 8 weeks ago Giovanni Calice ▴ 160
1
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0
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186
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Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data
11 weeks ago BioinfoMug • 0
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0
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179
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GDC slides download
TCGAbiolinks
3 months ago jain72744 • 0
0
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4
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317
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I need to calculate the survival rate of TCGA databases
TCGAbiolinks Survival
updated 3 months ago by ▴ 730 • written 3 months ago by • 0
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0
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171
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champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks ChAMP
3 months ago Thalita • 0
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1
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430
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Problems when running GDC_prepare in R
TCGAbiolinks error GDC_prepare
6 months ago leon • 0
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0
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257
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Where/how are TCGAbiolinks colData column names sourced from?
clinical TCGAbiolinks
10 months ago BioInfoBeginnerrr • 0
4
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8
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1.2k
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TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago Habil Zare ▴ 200
0
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2
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888
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RPPA data (Proteomics analysis)
TCGAbiolinks limma
13 months ago • updated 12 months ago qiz218591 • 0
1
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1
reply
793
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Error when running getGDCprojects()
TCGAbiolinks
14 months ago DevelopingHippo • 0
0
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1
reply
633
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 9 months ago by • 0 • written 14 months ago by ▴ 20
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0
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578
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
14 months ago Manav • 0
1
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2
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1.6k
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Error when running GDC_prepare
TCGAbiolinks
14 months ago DevelopingHippo • 0
1
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3
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959
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Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2 TCGAbiolinks
16 months ago Alexandre • 0
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0
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471
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TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
18 months ago lescano ▴ 10
0
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0
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654
views
Query on TCGA
TCGAbiolinks TCGAWorkflow
20 months ago hemangininaik09 • 0
0
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2
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1.4k
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Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 21 months ago by ▴ 270 • written 22 months ago by • 0
0
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0
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749
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About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
21 months ago qiz218591 • 0
0
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0
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539
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TCGAbiolinks file.type argument
TCGAbiolinks
22 months ago Elizabeth • 0
0
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0
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550
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Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks TCGAbiolinksGUI.data SummarizedExperiment
23 months ago syednajeebashraf • 0
5
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4
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2.9k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 2.0 years ago by ★ 1.4k • written 2.1 years ago by ▴ 30
0
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4
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1.0k
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GDCdownload Directory Problem :(
TCGAWorkflowData TCGAbiolinks
updated 12 weeks ago by 690 • written 2.0 years ago by • 0
0
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2
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2.1k
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GDCprepare error in TARGET-AML data access
TCGAbiolinks TARGET-AML
updated 2.1 years ago by ▴ 270 • written 2.1 years ago by • 0
0
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1
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1.9k
views
GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 20 months ago by • 0 • written 2.1 years ago by • 0
3
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2
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2.2k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.1 years ago by • 0 • written 5.5 years ago by ▴ 10
2
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5
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1.6k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
updated 2.1 years ago by • 0 • written 3.7 years ago by ▴ 40
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0
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582
views
GDCquery error when querying mutect2 data
TCGAbiolinks
2.1 years ago komal.rathi ▴ 120
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2
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2.1k
views
GDCprepare() - R Session Aborted
TCGAbiolinks R GDCprepare()
2.1 years ago • updated 19 months ago spyrouglykeria • 0
6
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3
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3.2k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 2.1 years ago by • 0 • written 2.1 years ago by ▴ 10
2
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8
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4.9k
views
GDCquery_Maf error
TCGAbiolinks GDCquery_Maf
updated 21 months ago by • 0 • written 2.1 years ago by • 0
0
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0
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827
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Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
2.4 years ago constantinosdem • 0
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0
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677
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq TCGAbiolinks TCGAAnalyze_DEA
2.5 years ago Gandino • 0
0
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1
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2.1k
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
2.5 years ago raf4 ▴ 20
1
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2
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1.1k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks cnv
2.6 years ago • updated 2.5 years ago raf4 ▴ 20
0
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1
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1.3k
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pre-proccessing of TCGA data for WGCNA
TCGAbiolinks WGCNA
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
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0
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739
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DEGs for legacy and harmonized dataset
#DEGs #legacydataset #harmonizeddataset TCGAbiolinks
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
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1
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1.2k
views
Help With TCGAbiolinks package
TCGAbiolinks data normalize l
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
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2
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1.2k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
3.0 years ago H. Z. Amini ▴ 10
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0
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1.6k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks TCGAWorkflowData
3.0 years ago H. Z. Amini ▴ 10
0
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0
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741
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
3.0 years ago rebeliscu • 0
0
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3
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949
views
discrepancy in number of samples
TCGAquery_recount2 TCGAbiolinks
3.1 years ago xiaofeiwang18266 ▴ 50
1
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1
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1.4k
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks RECOUNT2 DESeq2
updated 3.1 years ago by 42k • written 3.1 years ago by ▴ 50
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8
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3.5k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
3.1 years ago xiaofeiwang18266 ▴ 50
0
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0
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857
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
3.1 years ago martin.schaefer • 0
0
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1
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821
views
library(TCGAbiolinks)
TCGAbiolinks
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by • 0
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1
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1.7k
views
TCGAbiolinks connection error for GDCquery
MethylationArray TCGAbiolinks
3.3 years ago Sophie Marion de Proce • 0
0
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1
reply
911
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 3.4 years ago by 3.9k • written 3.4 years ago by • 0
0
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5
replies
2.1k
views
TCGA: to extract clinical data from barcode
cancer TCGAbiolinks
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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