Showing : tcga • reset
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98
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TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 8 weeks ago by ★ 2.0k • written 8 weeks ago by • 0
2
votes
9
replies
777
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
7 months ago Peipei • 0
2
votes
2
replies
462
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Create TPM gene tables/dataframe from ReCount3
recount3 TCGA GTEx DESeq2
7 months ago David ▴ 20
3
votes
2
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1.4k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 9 months ago by • 0 • written 4.2 years ago by ▴ 10
2
votes
5
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821
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
updated 9 months ago by • 0 • written 2.4 years ago by ▴ 40
1
vote
1
reply
446
views
recount3 - download bigwig files for TCGA data
recount3 recount TCGA
updated 10 months ago by ★ 1.0k • written 10 months ago by ▴ 10
0
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2
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408
views
Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
12 months ago IamFrofro • 0
3
votes
2
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528
views
How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA GenomicDataCommons
updated 14 months ago by ★ 3.0k • written 14 months ago by ▴ 10
5
votes
9
replies
1.9k
views
Error via running GDCquey from TCGAbiolinks package
TCGA Genome Data Common portal
updated 20 months ago by • 0 • written 4.6 years ago by ▴ 10
0
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0
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343
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
20 months ago rebeliscu • 0
0
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1
reply
407
views
Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA GenomicDataCommons
22 months ago Ezgi ▴ 30
0
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0
replies
561
views
Job: PhD position in Developmental Neurobiology and Bioinformatics
rnaseq neurobiology tcga Job
2.3 years ago Laurent Gatto 1.6k
0
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0
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383
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Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER TCGA GEO
2.4 years ago andrade4beatriz • 0
0
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5
replies
1.1k
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 2.4 years ago by ▴ 260 • written 2.4 years ago by ▴ 40
7
votes
17
replies
1.8k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation qsea MEDIPS TCGA
updated 2.5 years ago by ▴ 220 • written 5.8 years ago by ▴ 20
4
votes
7
replies
2.2k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 2.7 years ago by 3.7k • written 2.7 years ago by • 0
0
votes
2
replies
823
views
Recount2 Bigwigs for TCGA
R TCGA recount2 recount
updated 2.8 years ago by ★ 1.0k • written 2.9 years ago by • 0
4
votes
7
replies
479
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 2.8 years ago by 62k • written 2.8 years ago by ▴ 50
0
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0
replies
414
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks GDC TCGA
3.1 years ago modarzi ▴ 10
0
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4
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625
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks TCGA GDC
3.2 years ago modarzi ▴ 10
2
votes
3
replies
441
views
DESeq2 doesn't return the most drastically DEG
deseq2 tcga
3.2 years ago ndjayne • 0
2
votes
2
replies
785
views
DESeq2: design = ~1 For Normalisation Only.
deseq2 limma normalization tcga rnaseq
updated 3.3 years ago by 39k • written 3.3 years ago by • 0
1
vote
2
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623
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga bisulfite tcgabiolinks
updated 3.6 years ago by ▴ 260 • written 3.6 years ago by • 0
1
vote
1
reply
697
views
TCGA isoform expression quantification file - how to reshape data
data.frame tcga reshape data
updated 3.7 years ago by 13k • written 3.7 years ago by ▴ 160
1
vote
2
replies
826
views
TCGA MAF (Mutations) data
TCGA MAF GDC snp mutations
updated 3.7 years ago by 21k • written 3.7 years ago by ▴ 160
0
votes
1
reply
610
views
How to download the TCGA SKCM subtype information?
TCGA melanoma TCGA SKCM
3.7 years ago syrttgump ▴ 20
4
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4
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1.1k
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 3.8 years ago by 1.1k • written 3.8 years ago by ▴ 800
0
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0
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538
views
TCGAbiolinks specific mutation query
TCGAbiolinks TCGA Mutation GDCquery rnaseq
3.9 years ago Yonatan Amzaleg • 0
1
vote
3
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1.0k
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks TCGA Download
updated 3.9 years ago by ▴ 260 • written 3.9 years ago by ▴ 10
4
votes
6
replies
2.6k
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 3.9 years ago by 39k • written 3.9 years ago by ▴ 70
1
vote
5
replies
974
views
Issue with TCGAbiolinks package.
TCGA GDCprepare
4.0 years ago salvocomplicazioni1 • 0
0
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0
replies
441
views
Reference for minimum number of probes commonly used for segmentation of microarray data
segmentation reference CNA TCGA
4.0 years ago jlarsen728 • 0
4
votes
2
replies
684
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons tcga gdc rest http
updated 4.0 years ago by 21k • written 4.0 years ago by ▴ 20
0
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0
replies
681
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA geneset RNASeq TCGA subtypes
4.0 years ago Pietro ▴ 40
0
votes
0
replies
482
views
GDC RNA seq files (replicates?)
gdc data TCGA gdcdownload
4.1 years ago coyoung ▴ 10
2
votes
4
replies
735
views
edgeR. Known cancer genes are not differentially expressed?
edger tcga
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 20
0
votes
1
reply
755
views
RNAseq gene expression analysis in Personalized genomics
TCGA deseq2 edger limma
updated 4.2 years ago by 39k • written 4.2 years ago by • 0
2
votes
3
replies
922
views
Problem for finding "Locus Link ID" from Annotation file
wgcna package TCGA LocusLinkID genecode ensembl
updated 4.3 years ago by 62k • written 4.3 years ago by ▴ 10
8
votes
12
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3.7k
views
MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
multiassayexperiment wide format TCGA
updated 4.3 years ago by 620 • written 4.3 years ago by ▴ 160
8
votes
8
replies
4.4k
views
Voom transformation from counts and normalization to negative values
rnaseq voom limma tcga statistics
updated 4.3 years ago by 7.8k • written 4.3 years ago by ▴ 50
1
vote
2
replies
722
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 4.3 years ago by 47k • written 4.3 years ago by • 0
3
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4
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1.4k
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks tcga genomicdatacommon
4.4 years ago franceschini.gianmarco • 0
0
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5
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1.3k
views
DNA methylation analysis without raw data IDAT files
r illimina 450k methylation minfi champ tcga
updated 4.4 years ago by ▴ 250 • written 4.4 years ago by ▴ 50
4
votes
2
replies
1.3k
views
Where to download expected counts instead of normalized RSEM for TCGA LUAD?
limma tcga
updated 4.5 years ago by 13k • written 4.5 years ago by ▴ 50
0
votes
2
replies
2.0k
views
Error: vector memory exhausted (limit reached?)
tcgabiolinks tcga cnv mac os x gaia
updated 4.5 years ago by ▴ 20 • written 4.5 years ago by ▴ 20
6
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7
replies
1.1k
views
Download TCGA dataset like a S4 object
dataset tcga
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by ▴ 20
0
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0
replies
557
views
Noise Analyses of CNV Data from TCGA
tcgabiolinks tcga cnv noise pruning
4.6 years ago jrlarsen ▴ 10
8
votes
5
replies
1.2k
views
Querying specific TCGA datasets through the MultiAssayExperiment R package
MultiAssayExperiment curatedCRCdata multiomics TCGA
updated 4.6 years ago by 620 • written 4.6 years ago by ▴ 800
2
votes
1
reply
1.7k
views
Error in TCGAquery of TCGAbiolinks Package
software error bioconductor tcgabiolinks tcga r
updated 4.7 years ago by ▴ 90 • written 4.7 years ago by ▴ 50
0
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0
replies
871
views
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
deseq2 tcga
updated 4.7 years ago by 39k • written 4.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: transcript name mapping between human and mouse by Eric • 0
It works very well, and thanks for such a great answer! Because I use the old version gtf from GENECODE (vM12), the id version does not mat…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Votes
Answer: transcript name mapping between human and mouse
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
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