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tcga
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0
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TCGA RNAseq Normalization
normalization
RNASEQ
Normalization
TCGAutils
TCGA
updated 8 weeks ago by
ATpoint
★ 2.0k • written 8 weeks ago by
Deniz
• 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
views
Create TPM gene tables/dataframe from ReCount3
recount3
TCGA
GTEx
DESeq2
7 months ago
David
▴ 20
3
votes
2
replies
1.4k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 9 months ago by
cute scientist
• 0 • written 4.2 years ago by
Antonio Ahn
▴ 10
2
votes
5
replies
821
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks
TCGA
updated 9 months ago by
biologsr
• 0 • written 2.4 years ago by
aush
▴ 40
1
vote
1
reply
446
views
recount3 - download bigwig files for TCGA data
recount3
recount
TCGA
updated 10 months ago by
Leonardo Collado Torres
★ 1.0k • written 10 months ago by
Xuebing
▴ 10
0
votes
2
replies
408
views
Removing paired samples for DESeq2 analysis
RNASeq
DifferentialExpression
DESeq2
tcga
12 months ago
IamFrofro
• 0
3
votes
2
replies
528
views
How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA
GenomicDataCommons
updated 14 months ago by
Robert Castelo
★ 3.0k • written 14 months ago by
Hashirama
▴ 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
H. Z. Amini
• 0 • written 4.6 years ago by
modarzi
▴ 10
0
votes
0
replies
343
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA
TCGAbiolinks
20 months ago
rebeliscu
• 0
0
votes
1
reply
407
views
Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA
GenomicDataCommons
22 months ago
Ezgi
▴ 30
0
votes
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
votes
0
replies
383
views
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
votes
5
replies
1.1k
views
Retrieve TCGA expression data for a single gene
TCGA
TCGAbiolinks
updated 2.4 years ago by
Tiago Chedraoui Silva
▴ 260 • written 2.4 years ago by
aush
▴ 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
Matthias Lienhard
▴ 220 • written 5.8 years ago by
justinburgener
▴ 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
Kevin Blighe
3.7k • written 2.7 years ago by
J. Smith
• 0
0
votes
2
replies
823
views
Recount2 Bigwigs for TCGA
R
TCGA
recount2
recount
updated 2.8 years ago by
Leonardo Collado Torres
★ 1.0k • written 2.9 years ago by
alex.v.nesta
• 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
James W. MacDonald
62k • written 2.8 years ago by
fawazfebin
▴ 50
0
votes
0
replies
414
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks
GDC
TCGA
3.1 years ago
modarzi
▴ 10
0
votes
4
replies
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
Michael Love
39k • written 3.3 years ago by
Alex Greenshields-Watson
• 0
1
vote
2
replies
623
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga
bisulfite
tcgabiolinks
updated 3.6 years ago by
Tiago Chedraoui Silva
▴ 260 • written 3.6 years ago by
DS
• 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
Steve Lianoglou
13k • written 3.7 years ago by
mario.zanfardino
▴ 160
1
vote
2
replies
826
views
TCGA MAF (Mutations) data
TCGA
MAF
GDC
snp
mutations
updated 3.7 years ago by
Sean Davis
21k • written 3.7 years ago by
mario.zanfardino
▴ 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
votes
4
replies
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
Levi Waldron
1.1k • written 3.8 years ago by
svlachavas
▴ 800
0
votes
0
replies
538
views
TCGAbiolinks specific mutation query
TCGAbiolinks
TCGA
Mutation
GDCquery
rnaseq
3.9 years ago
Yonatan Amzaleg
• 0
1
vote
3
replies
1.0k
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks
TCGA
Download
updated 3.9 years ago by
Tiago Chedraoui Silva
▴ 260 • written 3.9 years ago by
modarzi
▴ 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
Michael Love
39k • written 3.9 years ago by
Marc Saric
▴ 70
1
vote
5
replies
974
views
Issue with TCGAbiolinks package.
TCGA
GDCprepare
4.0 years ago
salvocomplicazioni1
• 0
0
votes
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
Sean Davis
21k • written 4.0 years ago by
mk
▴ 20
0
votes
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
Aaron Lun
★ 28k • written 4.1 years ago by
rina
▴ 20
0
votes
1
reply
755
views
RNAseq gene expression analysis in Personalized genomics
TCGA
deseq2
edger
limma
updated 4.2 years ago by
Michael Love
39k • written 4.2 years ago by
bioc.vkas
• 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
James W. MacDonald
62k • written 4.3 years ago by
modarzi
▴ 10
8
votes
12
replies
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
Marcel Ramos
620 • written 4.3 years ago by
mario.zanfardino
▴ 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
Ryan C. Thompson
7.8k • written 4.3 years ago by
Beginner
▴ 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
Gordon Smyth
47k • written 4.3 years ago by
ZihaoXing
• 0
3
votes
4
replies
1.4k
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks
tcga
genomicdatacommon
4.4 years ago
franceschini.gianmarco
• 0
0
votes
5
replies
1.3k
views
DNA methylation analysis without raw data IDAT files
r
illimina 450k methylation
minfi
champ
tcga
updated 4.4 years ago by
Yuan Tian
▴ 250 • written 4.4 years ago by
Beginner
▴ 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
Steve Lianoglou
13k • written 4.5 years ago by
Ahdee
▴ 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
rreck
▴ 20 • written 4.5 years ago by
rina
▴ 20
6
votes
7
replies
1.1k
views
Download TCGA dataset like a S4 object
dataset
tcga
updated 4.5 years ago by
mario.zanfardino
▴ 160 • written 4.5 years ago by
Giuseppe
▴ 20
0
votes
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
Marcel Ramos
620 • written 4.6 years ago by
svlachavas
▴ 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
Benjamin Ostendorf
▴ 90 • written 4.7 years ago by
Beginner
▴ 50
0
votes
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
Michael Love
39k • written 4.7 years ago by
kcl
• 0
50 results • Page
1 of 1
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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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