Showing : TCGABiolinks • reset
1
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1
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1.3k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
1
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2
replies
1.5k
views
Error in retrieving clinical data
TCGAbiolinks
8 months ago silickas • 0
0
votes
1
reply
597
views
combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 10 months ago by • 0 • written 10 months ago by • 0
0
votes
7
replies
1.5k
views
How should I know which platforms are available for TCGA methylation?
TCGAbiolinks
updated 12 months ago by 68k • written 13 months ago by • 0
3
votes
3
replies
4.2k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error maftools tcgabiolinks
updated 20 months ago by ▴ 200 • written 8.1 years ago by ▴ 100
0
votes
0
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609
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
20 months ago Giovanni Calice ▴ 160
0
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0
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1.0k
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GDC slides download
TCGAbiolinks
21 months ago jain72744 • 0
0
votes
4
replies
1.3k
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks Survival
updated 21 months ago by ▴ 760 • written 21 months ago by • 0
0
votes
0
replies
655
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks ChAMP
21 months ago Thalita • 0
0
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1
reply
1.5k
views
Problems when running GDC_prepare in R
TCGAbiolinks error GDC_prepare
2.1 years ago leon • 0
0
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0
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640
views
Where/how are TCGAbiolinks colData column names sourced from?
clinical TCGAbiolinks
2.3 years ago BioInfoBeginnerrr • 0
4
votes
8
replies
2.1k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
2.5 years ago • updated 2.4 years ago Habil Zare ▴ 200
0
votes
2
replies
1.7k
views
RPPA data (Proteomics analysis)
TCGAbiolinks limma
2.6 years ago • updated 2.5 years ago qiz218591 • 0
1
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1
reply
1.3k
views
Error when running getGDCprojects()
TCGAbiolinks
2.7 years ago DevelopingHippo • 0
2
votes
1
reply
1.4k
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 2.2 years ago by • 0 • written 2.7 years ago by ▴ 200
0
votes
0
replies
1.3k
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
2.7 years ago Manav • 0
1
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2
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2.7k
views
Error when running GDC_prepare
TCGAbiolinks
2.7 years ago DevelopingHippo • 0
1
vote
3
replies
1.6k
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2 TCGAbiolinks
2.9 years ago Alexandre • 0
0
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0
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837
views
TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
3.0 years ago lescano ▴ 10
0
votes
0
replies
1.1k
views
Query on TCGA
TCGAbiolinks TCGAWorkflow
3.2 years ago hemangininaik09 • 0
0
votes
2
replies
2.6k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 3.3 years ago by ▴ 270 • written 3.4 years ago by • 0
0
votes
0
replies
1.3k
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
3.3 years ago qiz218591 • 0
0
votes
0
replies
1.0k
views
TCGAbiolinks file.type argument
TCGAbiolinks
3.3 years ago Elizabeth • 0
0
votes
0
replies
890
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks TCGAbiolinksGUI.data SummarizedExperiment
3.5 years ago syednajeebashraf • 0
5
votes
4
replies
4.5k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 3.5 years ago by ★ 1.4k • written 3.6 years ago by ▴ 30
0
votes
4
replies
1.8k
views
GDCdownload Directory Problem :(
TCGAWorkflowData TCGAbiolinks
updated 21 months ago by 700 • written 3.5 years ago by • 0
0
votes
2
replies
2.7k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks TARGET-AML
updated 3.6 years ago by ▴ 270 • written 3.6 years ago by • 0
0
votes
1
reply
2.5k
views
GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 3.2 years ago by • 0 • written 3.6 years ago by • 0
3
votes
2
replies
3.1k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 3.6 years ago by • 0 • written 7.0 years ago by ▴ 10
4
votes
5
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2.3k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
updated 3.6 years ago by • 0 • written 5.2 years ago by ▴ 40
0
votes
0
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1.1k
views
GDCquery error when querying mutect2 data
TCGAbiolinks
3.6 years ago komal.rathi ▴ 120
0
votes
2
replies
2.8k
views
GDCprepare() - R Session Aborted
TCGAbiolinks R GDCprepare()
3.6 years ago • updated 3.1 years ago spyrouglykeria • 0
6
votes
3
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4.0k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 3.6 years ago by • 0 • written 3.6 years ago by ▴ 10
2
votes
8
replies
6.6k
views
GDCquery_Maf error
TCGAbiolinks GDCquery_Maf
updated 3.3 years ago by • 0 • written 3.6 years ago by • 0
0
votes
1
reply
1.5k
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
updated 8 months ago by • 0 • written 3.9 years ago by • 0
0
votes
0
replies
1.2k
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq TCGAbiolinks TCGAAnalyze_DEA
4.0 years ago Gandino • 0
0
votes
1
reply
3.0k
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
4.0 years ago raf4 ▴ 30
1
vote
2
replies
1.9k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks cnv
4.1 years ago • updated 4.0 years ago raf4 ▴ 30
0
votes
1
reply
2.1k
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks WGCNA
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
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0
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1.1k
views
DEGs for legacy and harmonized dataset
#DEGs #legacydataset #harmonizeddataset TCGAbiolinks
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
0
votes
1
reply
1.7k
views
Help With TCGAbiolinks package
TCGAbiolinks data normalize l
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
0
votes
2
replies
1.8k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
4.5 years ago H. Z. Amini ▴ 10
0
votes
0
replies
2.7k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks TCGAWorkflowData
4.5 years ago H. Z. Amini ▴ 10
0
votes
0
replies
1.2k
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
4.5 years ago rebeliscu • 0
0
votes
3
replies
1.5k
views
discrepancy in number of samples
TCGAquery_recount2 TCGAbiolinks
4.6 years ago xiaofeiwang18266 ▴ 60
1
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1
reply
1.9k
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks RECOUNT2 DESeq2
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 60
3
votes
8
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4.7k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
4.6 years ago xiaofeiwang18266 ▴ 60
0
votes
0
replies
1.3k
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
4.6 years ago martin.schaefer • 0
0
votes
1
reply
1.2k
views
library(TCGAbiolinks)
TCGAbiolinks
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by • 0
0
votes
1
reply
2.7k
views
TCGAbiolinks connection error for GDCquery
MethylationArray TCGAbiolinks
4.8 years ago Sophie Marion de Proce • 0
165 results • Page 1 of 4
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Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
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Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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