Showing : TCGABiolinks • reset
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TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks TCGA clinical TCGA-BRCA
written 6 weeks ago by • 0
0
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0
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139
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
7 weeks ago • updated 5 weeks ago Giovanni Calice ▴ 160
1
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0
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158
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Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data
8 weeks ago BioinfoMug • 0
0
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0
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156
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GDC slides download
TCGAbiolinks
9 weeks ago jain72744 • 0
0
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4
replies
279
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I need to calculate the survival rate of TCGA databases
TCGAbiolinks Survival
updated 10 weeks ago by ▴ 730 • written 10 weeks ago by • 0
0
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0
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145
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks ChAMP
12 weeks ago Thalita • 0
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1
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385
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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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245
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Where/how are TCGAbiolinks colData column names sourced from?
clinical TCGAbiolinks
9 months ago BioInfoBeginnerrr • 0
4
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8
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1.2k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago • updated 10 months ago Habil Zare ▴ 200
0
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2
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849
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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
757
views
Error when running getGDCprojects()
TCGAbiolinks
13 months ago DevelopingHippo • 0
0
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1
reply
614
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How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 8 months ago by • 0 • written 13 months ago by ▴ 20
0
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0
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539
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
13 months ago Manav • 0
1
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2
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1.5k
views
Error when running GDC_prepare
TCGAbiolinks
14 months ago DevelopingHippo • 0
1
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3
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936
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2 TCGAbiolinks
15 months ago Alexandre • 0
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0
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459
views
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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634
views
Query on TCGA
TCGAbiolinks TCGAWorkflow
20 months ago hemangininaik09 • 0
0
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0
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719
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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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518
views
TCGAbiolinks file.type argument
TCGAbiolinks
21 months ago Elizabeth • 0
0
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2
replies
1.3k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 20 months ago by ▴ 270 • written 22 months ago by • 0
0
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0
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537
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Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks TCGAbiolinksGUI.data SummarizedExperiment
23 months ago syednajeebashraf • 0
0
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4
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980
views
GDCdownload Directory Problem :(
TCGAWorkflowData TCGAbiolinks
updated 9 weeks ago by 690 • written 24 months ago by • 0
0
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1
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1.9k
views
GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 19 months ago by • 0 • written 2.0 years ago by • 0
0
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2
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2.1k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks TARGET-AML
updated 24 months ago by ▴ 270 • written 2.0 years ago by • 0
0
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0
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568
views
GDCquery error when querying mutect2 data
TCGAbiolinks
2.0 years ago komal.rathi ▴ 120
0
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2
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2.1k
views
GDCprepare() - R Session Aborted
TCGAbiolinks R GDCprepare()
2.0 years ago • updated 18 months ago spyrouglykeria • 0
6
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3
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3.1k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 2.0 years ago by • 0 • written 2.1 years ago by ▴ 10
5
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4
replies
2.8k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 23 months ago by ★ 1.3k • written 2.1 years ago by ▴ 30
2
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8
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4.8k
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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801
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Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
2.4 years ago constantinosdem • 0
0
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0
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668
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq TCGAbiolinks TCGAAnalyze_DEA
2.4 years ago Gandino • 0
0
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1
reply
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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1.0k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks cnv
2.5 years ago raf4 ▴ 20
0
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1
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1.3k
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks WGCNA
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
0
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0
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709
views
DEGs for legacy and harmonized dataset
#DEGs #legacydataset #harmonizeddataset TCGAbiolinks
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
0
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1
reply
1.1k
views
Help With TCGAbiolinks package
TCGAbiolinks data normalize l
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
0
votes
2
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1.1k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
2.9 years ago H. Z. Amini ▴ 10
0
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0
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1.6k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks TCGAWorkflowData
2.9 years ago H. Z. Amini ▴ 10
0
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0
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727
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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929
views
discrepancy in number of samples
TCGAquery_recount2 TCGAbiolinks
3.0 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 3.0 years ago by 41k • written 3.0 years ago by ▴ 50
3
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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 • updated 3.0 years ago xiaofeiwang18266 ▴ 50
0
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0
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844
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
3.1 years ago martin.schaefer • 0
0
votes
1
reply
806
views
library(TCGAbiolinks)
TCGAbiolinks
updated 3.2 years ago by ★ 3.9k • written 3.2 years ago by • 0
0
votes
1
reply
1.7k
views
TCGAbiolinks connection error for GDCquery
MethylationArray TCGAbiolinks
3.3 years ago • updated 3.2 years ago Sophie Marion de Proce • 0
0
votes
1
reply
902
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 3.4 years ago by 3.8k • written 3.4 years ago by • 0
2
votes
5
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1.5k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
updated 2.0 years ago by • 0 • written 3.6 years ago by ▴ 40
0
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5
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2.0k
views
TCGA: to extract clinical data from barcode
cancer TCGAbiolinks
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by ▴ 10
0
votes
5
replies
2.7k
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 3.6 years ago by ▴ 260 • written 3.7 years ago by ▴ 40
4
votes
6
replies
1.7k
views
TCGABiolinks downloaded data do not match GDC portal data
TCGAbiolinks
3.7 years ago mario.zanfardino ▴ 160
50 results • Page 1 of 1
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Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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