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derfinder
•
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0
votes
6
replies
1.9k
views
derfinder and BAM indexes
derfinder
9.6 years ago
jessica.hekman
▴ 40
8
votes
31
replies
4.4k
views
derfinder: analyzeChr() breaks on chromosomes > 22
derfinder
9.5 years ago
jessica.hekman
▴ 40
1
vote
2
replies
1.3k
views
derfinder on bacteria PE strand specific RNA-seq
derfinder
7.5 years ago
eva.pinatel
▴ 10
2
votes
6
replies
2.2k
views
derfinder gets stuck in calculatePvalues
derfinder
software error
rnaseq
8.9 years ago
drramki.chop
• 0
9
votes
20
replies
2.7k
views
derfinder: analyzeChr() freezes in f-stat calculation
derfinder
updated 9.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.1 years ago by
jessica.hekman
▴ 40
3
votes
2
replies
985
views
DESeq2 normalization when using with derfinder
Normalization
DESeq2
derfinder
2.6 years ago • updated 2.5 years ago
Debayan
▴ 20
5
votes
20
replies
3.1k
views
derfinder: fullCoverage() problems
derfinder
updated 9.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.6 years ago by
jessica.hekman
▴ 40
1
vote
10
replies
2.4k
views
derfinder failing in mergeResults()
derfinder
updated 9.2 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.4 years ago by
jessica.hekman
▴ 40
0
votes
1
reply
1.7k
views
Error message suggestion for fullCoverage in derfinder
derfinder
updated 9.2 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.3 years ago by
jessica.hekman
▴ 40
4
votes
4
replies
1.1k
views
derfinder model.matrix with limma or single base-level F-statistics analysis
derfinder
2.8 years ago
Konstantinos Yeles
▴ 80
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
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
0
votes
1
reply
1.7k
views
error with base-level DERfinder using large sample sizes
derfinder
updated 7.2 years ago by
Leonardo Collado Torres
★ 1.0k • written 7.2 years ago by
andrewelamb
• 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
2
votes
1
reply
1.0k
views
Derinder options (species, annotations style)
derfinder
rnaseq
differential expression
updated 6.8 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.8 years ago by
fruce_ki
▴ 20
2
votes
1
reply
1.2k
views
Read normalization in derfinder
derfinder
normalization
rnaseq
updated 6.8 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.8 years ago by
helene.gylling
▴ 10
3
votes
13
replies
2.4k
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
0
votes
3
replies
1.2k
views
How to preserve the strand of coverage in derfinder::regionMatrix() ?
derfinder
updated 6.7 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.7 years ago by
fruce_ki
▴ 20
2
votes
1
reply
1.4k
views
derfinder mean Expressed Region cutoff
derfinder
updated 6.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.5 years ago by
António Miguel de Jesus Domingues
▴ 510
3
votes
3
replies
1.7k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder
recount
updated 6.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.5 years ago by
António Miguel de Jesus Domingues
▴ 510
3
votes
5
replies
1.2k
views
Detection of large regions of expression
derfinder
intergenic expression
updated 4.7 years ago by
Leonardo Collado Torres
★ 1.0k • written 4.7 years ago by
António Miguel de Jesus Domingues
▴ 510
2
votes
3
replies
1.4k
views
derfinder: mergeResults() running for three days and still going...
derfinder
9.5 years ago
jessica.hekman
▴ 40
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
23 results • Page
1 of 1
Recent ...
Replies
Answer: Can I trust the differential expression analysis when the two groups overlap on
by
Michael Love
42k
Can you use `vst` instead of `rlog` and increase to 1000 or 2000 genes? I'm wondering if there's a way to characterize these 7 samples. …
Comment: Can I trust the differential expression analysis when the two groups overlap on
by
BioinfGuru
▴ 30
I think I am about to run into the same issue with my data, so I'll be interested to read peoples opinions on this also i.e. when the group…
Answer: How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
by
Gordon Smyth
50k
The MDS plot shows that the time points are hugely different and whereas the replicate samples appear very consistent, with very low variat…
Answer: Store output of matchPWM()
by
mat149
▴ 70
hitlist<-lapply(irs, FUN = matchPWM, min.score="90%", with.score=TRUE, pwm = pwm) ot <- endoapply(hitlist, function(x) as(x, "IRanges")) …
Comment: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
alex.pico
▴ 20
Hi Matthew. Happy to help. The error message you are getting is indeed not very helpful. It's just saying that the CyREST return obj "res" …
Votes
Comment: Store output of matchPWM()
Answer: Store output of matchPWM()
Answer: Store output of matchPWM()
Answer: ChipQC 'names' attribute [9] must be the same length as the vector [2]'
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
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mat149
▴ 70
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Gordon Smyth
50k
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maria.soler
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Pietro
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neilzhao
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