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count matrix
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4
votes
10
replies
5.3k
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Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
rpkm
gene length
count matrix
edgeR
rsubread
8.6 years ago • updated 8.5 years ago
AB
▴ 110
4
votes
11
replies
2.3k
views
Enquiry about the summarizeOverlaps() function
summarizeoverlaps
summarizedexperiment
count matrix
low counts
rna-seq
updated 8.2 years ago by
Valerie Obenchain
★ 6.8k • written 8.2 years ago by
shania90.lk
▴ 10
0
votes
1
reply
1.8k
views
RSEM output in DeSeq2
RSEM
deseq2
count matrix
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
kmeusemann
• 0
3
votes
1
reply
4.7k
views
Creating a count matrix from 8 bam files in R (RNAseq experiment)
deseq2
rnaseq
count matrix
galignments
granges
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
bananaal1
▴ 10
2
votes
2
replies
7.3k
views
RNA STAR to DESeq2
deseq2
count matrix
star
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
nikelle.petrillo
• 0
0
votes
2
replies
1.4k
views
How to simulate a count matrix using Polyester
simulation
count matrix
RNA-seq
Polyester
updated 6.4 years ago by
Alyssa Frazee
▴ 210 • written 6.4 years ago by
fa.gholizadeh89
• 0
1
vote
1
reply
1.9k
views
How can I retrieve the gene names of my count matrix?
rnaseq
summarizeoverlaps
count matrix
updated 6.3 years ago by
James W. MacDonald
65k • written 6.3 years ago by
johnsonn573
• 0
1
vote
1
reply
826
views
count matrix from BAM file
count matrix
6.8 years ago
nosheenfaiz09
• 0
8 results • Page
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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. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
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…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
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
A: Print Differentially Expressed Exons From Dexseq Results
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