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tcga
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0
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1
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120
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 7 days ago by
BioinfoMug
• 0
1
vote
0
replies
98
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
21 days ago
BioinfoMug
• 0
7
votes
18
replies
2.9k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 10 weeks ago by
Matthias Lienhard
▴ 240 • written 7.0 years ago by
justinburgener
▴ 20
0
votes
2
replies
451
views
TCGA counts to TPM from recount3 do not seem to right
recount3
TCGA
RNASeq
updated 4 months ago by
Leonardo Collado Torres
★ 1.0k • written 4 months ago by
tangming2005
▴ 190
0
votes
1
reply
452
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA
GenomicDataCommons
GDC
written 8 months ago by
António Miguel de Jesus Domingues
▴ 490
1
vote
1
reply
437
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 8 months ago by
ATpoint
★ 3.9k • written 8 months ago by
khaserdene99
• 0
1
vote
3
replies
906
views
Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2
recount
GTEx
TCGA
recount3
updated 10 months ago by
ATpoint
★ 3.9k • written 10 months ago by
David
▴ 20
0
votes
1
reply
584
views
TCGA RNAseq Normalization
normalization
RNASEQ
Normalization
TCGAutils
TCGA
updated 15 months ago by
ATpoint
★ 3.9k • written 15 months ago by
Deniz
• 0
2
votes
9
replies
2.1k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA
r
RNASeqData
voom
limma
21 months ago
Peipei
• 0
2
votes
2
replies
1.8k
views
Create TPM gene tables/dataframe from ReCount3
recount3
TCGA
GTEx
DESeq2
21 months ago
David
▴ 20
3
votes
2
replies
2.1k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 23 months ago by
cute scientist
• 0 • written 5.3 years ago by
Antonio Ahn
▴ 10
2
votes
5
replies
1.5k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks
TCGA
updated 23 months ago by
biologsr
• 0 • written 3.5 years ago by
aush
▴ 40
1
vote
1
reply
991
views
recount3 - download bigwig files for TCGA data
recount3
recount
TCGA
updated 24 months ago by
Leonardo Collado Torres
★ 1.0k • written 24 months ago by
Xuebing
▴ 10
0
votes
2
replies
824
views
Removing paired samples for DESeq2 analysis
RNASeq
DifferentialExpression
DESeq2
tcga
2.1 years ago
IamFrofro
• 0
3
votes
2
replies
1.0k
views
How to obtain clinical data from TCGA via Bioconductor GenomicDataCommons
TCGA
GenomicDataCommons
updated 2.3 years ago by
Robert Castelo
★ 3.1k • written 2.3 years ago by
Hashirama
▴ 10
5
votes
9
replies
3.2k
views
Error via running GDCquey from TCGAbiolinks package
TCGA
Genome Data Common portal
updated 2.8 years ago by
H. Z. Amini
▴ 10 • written 5.7 years ago by
modarzi
▴ 10
0
votes
0
replies
685
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA
TCGAbiolinks
2.8 years ago
rebeliscu
• 0
0
votes
1
reply
767
views
Getting number of cases added by date to TCGA project with `GenomicDataCommons`
TCGA
GenomicDataCommons
3.0 years ago
Ezgi
▴ 60
0
votes
0
replies
919
views
Job:
PhD position in Developmental Neurobiology and Bioinformatics
rnaseq
neurobiology
tcga
Job
3.4 years ago
Laurent Gatto
1.6k
0
votes
0
replies
690
views
Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER
TCGA
GEO
3.5 years ago
andrade4beatriz
• 0
0
votes
5
replies
2.6k
views
Retrieve TCGA expression data for a single gene
TCGA
TCGAbiolinks
updated 3.5 years ago by
Tiago Chedraoui Silva
▴ 260 • written 3.5 years ago by
aush
▴ 40
4
votes
7
replies
3.7k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2
tximport
tcga
rsem
firebrowse
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
J. Smith
• 0
0
votes
2
replies
1.4k
views
Recount2 Bigwigs for TCGA
R
TCGA
recount2
recount
updated 4.0 years ago by
Leonardo Collado Torres
★ 1.0k • written 4.0 years ago by
alex.v.nesta
• 0
4
votes
7
replies
1.0k
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger
differential expression
TCGA
Gene ID
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
fawazfebin
▴ 60
0
votes
0
replies
684
views
Problem for downloading TCGA cancer data by TCGAbiolinks
TCGAbiolinks
GDC
TCGA
4.3 years ago
modarzi
▴ 10
0
votes
4
replies
1.1k
views
problem for downloading TCGA data by TCGAbiolikns package
TCGAbiolinks
TCGA
GDC
4.3 years ago
modarzi
▴ 10
2
votes
3
replies
772
views
DESeq2 doesn't return the most drastically DEG
deseq2
tcga
4.4 years ago
ndjayne
• 0
2
votes
2
replies
2.1k
views
DESeq2: design = ~1 For Normalisation Only.
deseq2
limma
normalization
tcga
rnaseq
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
Alex Greenshields-Watson
• 0
1
vote
2
replies
1.1k
views
TCGAbiolinks : Bisulfite-seq data : Legacy archive
tcga
bisulfite
tcgabiolinks
updated 4.7 years ago by
Tiago Chedraoui Silva
▴ 260 • written 4.7 years ago by
DS
• 0
1
vote
1
reply
1.2k
views
TCGA isoform expression quantification file - how to reshape data
data.frame
tcga
reshape data
updated 4.8 years ago by
Steve Lianoglou
★ 13k • written 4.8 years ago by
mario.zanfardino
▴ 160
1
vote
2
replies
1.3k
views
TCGA MAF (Mutations) data
TCGA
MAF
GDC
snp
mutations
updated 4.9 years ago by
Sean Davis
21k • written 4.9 years ago by
mario.zanfardino
▴ 160
0
votes
1
reply
1.1k
views
How to download the TCGA SKCM subtype information?
TCGA
melanoma
TCGA
SKCM
4.9 years ago
syrttgump
▴ 20
5
votes
4
replies
1.8k
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 5.0 years ago by
Levi Waldron
★ 1.1k • written 5.0 years ago by
svlachavas
▴ 830
0
votes
0
replies
921
views
TCGAbiolinks specific mutation query
TCGAbiolinks
TCGA
Mutation
GDCquery
rnaseq
5.0 years ago
Yonatan Amzaleg
• 0
1
vote
3
replies
2.0k
views
Error via running GDCdownload() in TCGAbiolinks
TCGAbiolinks
TCGA
Download
updated 5.0 years ago by
Tiago Chedraoui Silva
▴ 260 • written 5.0 years ago by
modarzi
▴ 10
4
votes
6
replies
3.4k
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 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
Marc Saric
▴ 70
1
vote
5
replies
1.5k
views
Issue with TCGAbiolinks package.
TCGA
GDCprepare
5.1 years ago
salvocomplicazioni1
• 0
0
votes
0
replies
772
views
Reference for minimum number of probes commonly used for segmentation of microarray data
segmentation
reference
CNA
TCGA
5.1 years ago
jlarsen728
• 0
4
votes
2
replies
1.1k
views
GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
genomicdatacommons
tcga
gdc
rest
http
updated 5.2 years ago by
Sean Davis
21k • written 5.2 years ago by
mk
▴ 20
0
votes
0
replies
998
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA
geneset
RNASeq
TCGA
subtypes
5.2 years ago
Pietro
▴ 40
0
votes
0
replies
867
views
GDC RNA seq files (replicates?)
gdc data
TCGA
gdcdownload
5.2 years ago
coyoung
▴ 10
2
votes
4
replies
1.2k
views
edgeR. Known cancer genes are not differentially expressed?
edger
tcga
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
rina
▴ 30
0
votes
1
reply
1.1k
views
RNAseq gene expression analysis in Personalized genomics
TCGA
deseq2
edger
limma
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
bioc.vkas
• 0
2
votes
3
replies
1.4k
views
Problem for finding "Locus Link ID" from Annotation file
wgcna package
TCGA
LocusLinkID
genecode
ensembl
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 years ago by
modarzi
▴ 10
8
votes
12
replies
6.0k
views
MultiAssayExperiment: Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
multiassayexperiment
wide format
TCGA
updated 5.5 years ago by
Marcel Ramos
680 • written 5.5 years ago by
mario.zanfardino
▴ 160
8
votes
8
replies
6.5k
views
Voom transformation from counts and normalization to negative values
rnaseq
voom
limma
tcga
statistics
updated 5.5 years ago by
Ryan C. Thompson
★ 7.9k • written 5.5 years ago by
Beginner
▴ 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 5.5 years ago by
Gordon Smyth
50k • written 5.5 years ago by
ZihaoXing
• 0
3
votes
4
replies
2.3k
views
TCGA biolinks - Samples with multiple profiles
tcgabiolinks
tcga
genomicdatacommon
5.6 years ago
franceschini.gianmarco
• 0
0
votes
5
replies
2.0k
views
DNA methylation analysis without raw data IDAT files
r
illimina 450k methylation
minfi
champ
tcga
updated 5.6 years ago by
Yuan Tian
▴ 270 • written 5.6 years ago by
Beginner
▴ 60
4
votes
2
replies
1.9k
views
Where to download expected counts instead of normalized RSEM for TCGA LUAD?
limma
tcga
updated 5.6 years ago by
Steve Lianoglou
★ 13k • written 5.6 years ago by
Ahdee
▴ 50
50 results • Page
1 of 1
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Replies
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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