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derfinder
•
reset
3
votes
2
replies
952
views
DESeq2 normalization when using with derfinder
Normalization
DESeq2
derfinder
2.4 years ago
Debayan
▴ 20
4
votes
4
replies
1.1k
views
derfinder model.matrix with limma or single base-level F-statistics analysis
derfinder
2.7 years ago
Konstantinos Yeles
▴ 80
3
votes
5
replies
1.2k
views
Detection of large regions of expression
derfinder
intergenic expression
updated 4.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 4.5 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 6.3 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.3 years ago by
António Miguel de Jesus Domingues
▴ 490
2
votes
1
reply
1.3k
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 6.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.6 years ago by
fruce_ki
▴ 20
2
votes
1
reply
1.2k
views
Read normalization in derfinder
derfinder
normalization
rnaseq
updated 6.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.6 years ago by
helene.gylling
▴ 10
2
votes
1
reply
999
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
1.2k
views
derfinder fullCoverage() changes chromosome style and then regionMatrix() complains and ignores provided 'currentStyle'
derfinder
6.9 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
6.9 years ago
Wayne
• 0
0
votes
1
reply
1.7k
views
error with base-level DERfinder using large sample sizes
derfinder
updated 7.0 years ago by
Leonardo Collado Torres
★ 1.0k • written 7.0 years ago by
andrewelamb
• 0
1
vote
10
replies
3.3k
views
Issue creating a genomic state object in derfinder from an Ensembl GTF file
derfinder
genomicfeatures
7.1 years ago
Leonardo Collado Torres
★ 1.0k
1
vote
2
replies
1.2k
views
derfinder on bacteria PE strand specific RNA-seq
derfinder
7.3 years ago
eva.pinatel
▴ 10
2
votes
6
replies
2.1k
views
derfinder gets stuck in calculatePvalues
derfinder
software error
rnaseq
8.8 years ago • updated 8.7 years ago
drramki.chop
• 0
0
votes
1
reply
1.4k
views
derfinder fails on findRegions step
derfinder
updated 8.8 years ago by
Leonardo Collado Torres
★ 1.0k • written 8.8 years ago by
pschaugh
• 0
9
votes
20
replies
2.6k
views
derfinder: analyzeChr() freezes in f-stat calculation
derfinder
updated 9.0 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.0 years ago by
jessica.hekman
▴ 40
0
votes
1
reply
1.6k
views
Error message suggestion for fullCoverage in derfinder
derfinder
updated 9.0 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.2 years ago by
jessica.hekman
▴ 40
1
vote
10
replies
2.3k
views
derfinder failing in mergeResults()
derfinder
updated 9.0 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.3 years ago by
jessica.hekman
▴ 40
8
votes
31
replies
4.3k
views
derfinder: analyzeChr() breaks on chromosomes > 22
derfinder
9.4 years ago
jessica.hekman
▴ 40
2
votes
3
replies
1.3k
views
derfinder: mergeResults() running for three days and still going...
derfinder
9.4 years ago
jessica.hekman
▴ 40
5
votes
20
replies
3.0k
views
derfinder: fullCoverage() problems
derfinder
updated 9.4 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.4 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
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Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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