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derfinder
•
reset
3
votes
2
replies
978
views
DESeq2 normalization when using with derfinder
Normalization
DESeq2
derfinder
2.5 years ago
Debayan
▴ 20
4
votes
4
replies
1.1k
views
derfinder model.matrix with limma or single base-level F-statistics analysis
derfinder
2.8 years ago • updated 2.7 years ago
Konstantinos Yeles
▴ 80
3
votes
5
replies
1.2k
views
Detection of large regions of expression
derfinder
intergenic expression
updated 4.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 4.6 years ago by
António Miguel de Jesus Domingues
▴ 490
3
votes
3
replies
1.7k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder
recount
updated 6.4 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.4 years ago by
António Miguel de Jesus Domingues
▴ 490
2
votes
1
reply
1.4k
views
derfinder mean Expressed Region cutoff
derfinder
updated 6.4 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.4 years ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
3
replies
1.2k
views
How to preserve the strand of coverage in derfinder::regionMatrix() ?
derfinder
updated 6.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.6 years ago by
fruce_ki
▴ 20
3
votes
13
replies
2.3k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder
genomicfeatures
genomicranges
updated 6.7 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.7 years ago by
fruce_ki
▴ 20
2
votes
1
reply
1.2k
views
Read normalization in derfinder
derfinder
normalization
rnaseq
updated 6.7 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.7 years ago by
helene.gylling
▴ 10
2
votes
1
reply
1.0k
views
Derinder options (species, annotations style)
derfinder
rnaseq
differential expression
updated 6.7 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.7 years ago by
fruce_ki
▴ 20
0
votes
1
reply
1.3k
views
derfinder fullCoverage() changes chromosome style and then regionMatrix() complains and ignores provided 'currentStyle'
derfinder
7.0 years ago
Wayne
• 0
0
votes
7
replies
2.0k
views
regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder
GenomeInfoDb
GenomicRanges
7.0 years ago
Wayne
• 0
0
votes
1
reply
1.7k
views
error with base-level DERfinder using large sample sizes
derfinder
updated 7.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 7.1 years ago by
andrewelamb
• 0
1
vote
10
replies
3.4k
views
Issue creating a genomic state object in derfinder from an Ensembl GTF file
derfinder
genomicfeatures
7.2 years ago
Leonardo Collado Torres
★ 1.0k
1
vote
2
replies
1.3k
views
derfinder on bacteria PE strand specific RNA-seq
derfinder
7.4 years ago
eva.pinatel
▴ 10
2
votes
6
replies
2.1k
views
derfinder gets stuck in calculatePvalues
derfinder
software error
rnaseq
8.9 years ago • updated 8.8 years ago
drramki.chop
• 0
0
votes
1
reply
1.5k
views
derfinder fails on findRegions step
derfinder
updated 8.9 years ago by
Leonardo Collado Torres
★ 1.0k • written 8.9 years ago by
pschaugh
• 0
9
votes
20
replies
2.7k
views
derfinder: analyzeChr() freezes in f-stat calculation
derfinder
updated 9.0 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.1 years ago by
jessica.hekman
▴ 40
0
votes
1
reply
1.7k
views
Error message suggestion for fullCoverage in derfinder
derfinder
updated 9.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.3 years ago by
jessica.hekman
▴ 40
1
vote
10
replies
2.3k
views
derfinder failing in mergeResults()
derfinder
updated 9.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.4 years ago by
jessica.hekman
▴ 40
8
votes
31
replies
4.3k
views
derfinder: analyzeChr() breaks on chromosomes > 22
derfinder
9.5 years ago
jessica.hekman
▴ 40
2
votes
3
replies
1.4k
views
derfinder: mergeResults() running for three days and still going...
derfinder
9.5 years ago
jessica.hekman
▴ 40
5
votes
20
replies
3.1k
views
derfinder: fullCoverage() problems
derfinder
updated 9.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.5 years ago by
jessica.hekman
▴ 40
0
votes
6
replies
1.9k
views
derfinder and BAM indexes
derfinder
9.5 years ago
jessica.hekman
▴ 40
23 results • Page
1 of 1
Recent ...
Replies
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…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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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Leo Lahti
▴ 40
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James W. MacDonald
65k
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to
shepherl
3.8k
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to
Michael Love
41k
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