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RNASeqRData
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1
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4
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809
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RNA-seq analysis between a wildtype vs a double microRNA kockout mouse brain
microRNA
gene
RNASeqRData
edgeR
geneontology
18 months ago
faiza
• 0
1
vote
3
replies
674
views
What should I do with RNA-Seq data to get a gene that work?
find
RNASeqRData
updated 18 months ago by
ATpoint
★ 4.1k • written 18 months ago by
yuhang
• 0
1
vote
4
replies
1.4k
views
merge TPM values for same geneID
RNASeqRData
TPM
updated 19 months ago by
ATpoint
★ 4.1k • written 19 months ago by
prashali.bansal
▴ 10
0
votes
0
replies
470
views
how to create PHENO_DATA
RNASeq
RNASeqData
RNASeqRData
20 months ago
marymshahi2021
• 0
0
votes
1
reply
600
views
DeSeq2 timecourse analysis
RNAseqRData
DeSeq2
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
Hannah
• 0
0
votes
17
replies
3.2k
views
results(dds) error: couldn't find results. you should first run DESeq()
RNASeqRData
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
beslinail
• 0
1
vote
1
reply
787
views
edgeR for SDE analysis
RNASeqRData
edgeR
RNASeqR
RNASeqData
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 years ago by
vikycairoli
• 0
1
vote
2
replies
884
views
Is 100K genes too many to run ComBat_seq on?
RNASeqRData
combat_Seq
BatchEffect
2.6 years ago • updated 2.3 years ago
zeegzaag
• 0
0
votes
1
reply
864
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData
limma
RNASeq
RNASeqR
updated 3.1 years ago by
Gordon Smyth
50k • written 3.1 years ago by
Rita
• 0
2
votes
2
replies
2.6k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData
GO
3.2 years ago
Wuschel
▴ 10
0
votes
0
replies
737
views
display .CT files in a BioC package
RNAinteract
rnaseqGene
RNASeqRData
rnaseqcomp
3.2 years ago
Bogdan
▴ 670
4
votes
4
replies
1.1k
views
DEseq2: working with unbalanced number of sample in tumor study?
Deseq2
RNASeqRData
unbalancedsamplesize
updated 23 months ago by
Michael Love
41k • written 3.2 years ago by
Cihat
• 0
1
vote
5
replies
2.1k
views
How can I use bioconductor and Deseq2 in linux ubuntu 18
RiboProfiling
DESeq2
Bioconductor
RNASeqRData
updated 18 months ago by
Kevin Blighe
★ 3.9k • written 3.3 years ago by
Taufiq
• 0
13 results • Page
1 of 1
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Replies
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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