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TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 16 days ago by
BioinfoMug
• 0
1
vote
0
replies
112
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
4 weeks 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 12 weeks ago by
Matthias Lienhard
▴ 240 • written 7.0 years ago by
justinburgener
▴ 20
0
votes
2
replies
469
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 5 months ago by
tangming2005
▴ 190
0
votes
1
reply
465
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA
GenomicDataCommons
GDC
written 9 months ago by
António Miguel de Jesus Domingues
▴ 490
1
vote
1
reply
452
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 9 months ago by
ATpoint
★ 4.0k • written 9 months ago by
khaserdene99
• 0
1
vote
3
replies
929
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
★ 4.0k • written 11 months ago by
David
▴ 20
7 results • Page
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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