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count matrix
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4
votes
10
replies
5.2k
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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
8.5 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 6.2 years ago by
James W. MacDonald
65k • written 6.2 years ago by
johnsonn573
• 0
1
vote
1
reply
822
views
count matrix from BAM file
count matrix
6.8 years ago
nosheenfaiz09
• 0
8 results • Page
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Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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