Showing : TCGA • reset
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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
9 days ago • updated 1 day ago glaciya2018 • 0
0
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1
reply
228
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TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks TCGA clinical TCGA-BRCA
written 7 weeks ago by • 0
1
vote
0
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174
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Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data
9 weeks ago BioinfoMug • 0
7
votes
18
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3.0k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 4 months ago by ▴ 240 • written 7.1 years ago by ▴ 20
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2
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535
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TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 5 months ago by ★ 1.0k • written 6 months ago by ▴ 190
0
votes
1
reply
508
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 10 months ago by ▴ 510
1
vote
1
reply
496
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
1
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3
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1.0k
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2 recount GTEx TCGA recount3
updated 12 months ago by ★ 4.1k • written 12 months ago by ▴ 20
0
votes
1
reply
633
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
2
votes
9
replies
2.3k
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Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
22 months ago Peipei • 0
2
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2
replies
1.9k
views
Create TPM gene tables/dataframe from ReCount3
recount3 TCGA GTEx DESeq2
23 months ago David ▴ 20
3
votes
2
replies
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 2.0 years ago by • 0 • written 3.6 years ago by ▴ 40
1
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1
reply
1.1k
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recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 2.1 years ago by ★ 1.0k • written 2.1 years ago by ▴ 10
0
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2
replies
890
views
Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
2.3 years ago IamFrofro • 0
3
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2
replies
1.1k
views
How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA GenomicDataCommons
updated 2.4 years ago by ★ 3.3k • written 2.4 years ago by ▴ 10
5
votes
9
replies
3.3k
views
Error via running GDCquey from TCGAbiolinks package
TCGA Genome Data Common portal
updated 2.9 years ago by ▴ 10 • written 5.9 years ago by ▴ 10
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0
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733
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Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
3.0 years ago rebeliscu • 0
0
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1
reply
817
views
Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA GenomicDataCommons
3.1 years ago Ezgi ▴ 60
0
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0
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956
views
Job: PhD position in Developmental Neurobiology and Bioinformatics
rnaseq neurobiology tcga Job
3.5 years ago Laurent Gatto 1.6k
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0
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723
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Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER TCGA GEO
3.7 years ago andrade4beatriz • 0
0
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5
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2.8k
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 3.7 years ago by ▴ 260 • written 3.7 years ago by ▴ 40
4
votes
7
replies
4.0k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 4.0 years ago by ★ 3.9k • written 4.0 years ago by • 0
0
votes
2
replies
1.4k
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 4.1 years ago by ★ 1.0k • written 4.2 years ago by • 0
4
votes
7
replies
1.1k
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 60
0
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0
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716
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
4.4 years ago modarzi ▴ 10
0
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4
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1.2k
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
4.4 years ago modarzi ▴ 10
2
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3
replies
805
views
DESeq2 doesn't return the most drastically DEG
deseq2 tcga
4.5 years ago ndjayne • 0
2
votes
2
replies
2.3k
views
DESeq2: design = ~1 For Normalisation Only.
deseq2 limma normalization tcga rnaseq
updated 4.5 years ago by 41k • written 4.5 years ago by • 0
1
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2
replies
1.2k
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga bisulfite tcgabiolinks
updated 4.8 years ago by ▴ 260 • written 4.8 years ago by • 0
1
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1
reply
1.3k
views
TCGA isoform expression quantification file - how to reshape data
data.frame tcga reshape data
updated 5.0 years ago by ★ 13k • written 5.0 years ago by ▴ 160
1
vote
2
replies
1.3k
views
TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 5.0 years ago by 21k • written 5.0 years ago by ▴ 160
0
votes
1
reply
1.1k
views
How to download the TCGA SKCM subtype information?
TCGA melanoma TCGA SKCM
5.0 years ago syrttgump ▴ 20
5
votes
4
replies
1.9k
views
Perform correlation analysis between miRNA and mRNA gene expression data on the same TCGA dataset based on the curatedTCGAData
curatedTCGAData MultiAssayExperiment multiomics TCGA
updated 5.1 years ago by ★ 1.1k • written 5.1 years ago by ▴ 830
0
votes
0
replies
980
views
TCGAbiolinks specific mutation query
TCGAbiolinks TCGA Mutation GDCquery rnaseq
5.1 years ago Yonatan Amzaleg • 0
1
vote
3
replies
2.1k
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks TCGA Download
updated 5.2 years ago by ▴ 260 • written 5.2 years ago by ▴ 10
4
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6
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3.6k
views
DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what can I do about it?
deseq2 normalization rna-seq TCGA vst
updated 5.2 years ago by 41k • written 5.2 years ago by ▴ 70
1
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5
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1.6k
views
Issue with TCGAbiolinks package.
TCGA GDCprepare
5.2 years ago salvocomplicazioni1 • 0
0
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0
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816
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Reference for minimum number of probes commonly used for segmentation of microarray data
segmentation reference CNA TCGA
5.2 years ago jlarsen728 • 0
4
votes
2
replies
1.1k
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 5.3 years ago by 21k • written 5.3 years ago by ▴ 20
0
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0
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1.0k
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA geneset RNASeq TCGA subtypes
5.3 years ago Pietro ▴ 40
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0
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917
views
GDC RNA seq files (replicates?)
gdc data TCGA gdcdownload
5.3 years ago coyoung ▴ 10
2
votes
4
replies
1.3k
views
edgeR. Known cancer genes are not differentially expressed?
edger tcga
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 30
0
votes
1
reply
1.1k
views
RNAseq gene expression analysis in Personalized genomics
TCGA deseq2 edger limma
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
2
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3
replies
1.5k
views
Problem for finding "Locus Link ID" from Annotation file
wgcna package TCGA LocusLinkID genecode ensembl
updated 5.5 years ago by 65k • written 5.5 years ago by ▴ 10
8
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12
replies
6.2k
views
MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
multiassayexperiment wide format TCGA
updated 5.6 years ago by 690 • written 5.6 years ago by ▴ 160
8
votes
8
replies
6.8k
views
Voom transformation from counts and normalization to negative values
rnaseq voom limma tcga statistics
updated 5.6 years ago by ★ 7.9k • written 5.6 years ago by ▴ 60
1
vote
2
replies
1.2k
views
how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?
deseq2 edger fpkm counts TCGA
updated 5.6 years ago by 50k • written 5.6 years ago by • 0
3
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4
replies
2.4k
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks tcga genomicdatacommon
5.7 years ago franceschini.gianmarco • 0
0
votes
5
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2.1k
views
DNA methylation analysis without raw data IDAT files
r illimina 450k methylation minfi champ tcga
updated 5.7 years ago by ▴ 280 • written 5.7 years ago by ▴ 60
50 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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