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derfinder
•
reset
3
votes
2
replies
1.2k
views
DESeq2 normalization when using with derfinder
Normalization
DESeq2
derfinder
3.1 years ago
Debayan
▴ 20
4
votes
4
replies
1.4k
views
derfinder model.matrix with limma or single base-level F-statistics analysis
derfinder
3.4 years ago
Konstantinos Yeles
▴ 80
3
votes
5
replies
1.5k
views
Detection of large regions of expression
derfinder
intergenic expression
updated 5.3 years ago by
Leonardo Collado Torres
★ 1.1k • written 5.3 years ago by
António Miguel de Jesus Domingues
▴ 510
3
votes
3
replies
2.0k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder
recount
updated 7.1 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.1 years ago by
António Miguel de Jesus Domingues
▴ 510
2
votes
1
reply
1.6k
views
derfinder mean Expressed Region cutoff
derfinder
updated 7.1 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.1 years ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
3
replies
1.5k
views
How to preserve the strand of coverage in derfinder::regionMatrix() ?
derfinder
updated 7.3 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.3 years ago by
fruce_ki
▴ 20
3
votes
13
replies
2.8k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder
genomicfeatures
genomicranges
updated 7.3 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.3 years ago by
fruce_ki
▴ 20
2
votes
1
reply
1.4k
views
Read normalization in derfinder
derfinder
normalization
rnaseq
updated 7.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.4 years ago by
helene.gylling
▴ 10
2
votes
1
reply
1.2k
views
Derinder options (species, annotations style)
derfinder
rnaseq
differential expression
updated 7.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.4 years ago by
fruce_ki
▴ 20
0
votes
1
reply
1.5k
views
derfinder fullCoverage() changes chromosome style and then regionMatrix() complains and ignores provided 'currentStyle'
derfinder
7.6 years ago
Wayne
• 0
0
votes
7
replies
2.4k
views
regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder
GenomeInfoDb
GenomicRanges
7.6 years ago
Wayne
• 0
0
votes
1
reply
1.9k
views
error with base-level DERfinder using large sample sizes
derfinder
updated 7.8 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.8 years ago by
andrewelamb
• 0
1
vote
10
replies
3.8k
views
Issue creating a genomic state object in derfinder from an Ensembl GTF file
derfinder
genomicfeatures
7.8 years ago
Leonardo Collado Torres
★ 1.1k
1
vote
2
replies
1.5k
views
derfinder on bacteria PE strand specific RNA-seq
derfinder
8.0 years ago
eva.pinatel
▴ 10
2
votes
6
replies
2.4k
views
derfinder gets stuck in calculatePvalues
derfinder
software error
rnaseq
9.5 years ago
drramki.chop
• 0
0
votes
1
reply
1.6k
views
derfinder fails on findRegions step
derfinder
updated 9.5 years ago by
Leonardo Collado Torres
★ 1.1k • written 9.5 years ago by
pschaugh
• 0
9
votes
20
replies
3.1k
views
derfinder: analyzeChr() freezes in f-stat calculation
derfinder
updated 9.7 years ago by
Leonardo Collado Torres
★ 1.1k • written 9.7 years ago by
jessica.hekman
▴ 40
0
votes
1
reply
1.8k
views
Error message suggestion for fullCoverage in derfinder
derfinder
updated 9.8 years ago by
Leonardo Collado Torres
★ 1.1k • written 9.9 years ago by
jessica.hekman
▴ 40
1
vote
10
replies
2.7k
views
derfinder failing in mergeResults()
derfinder
updated 9.8 years ago by
Leonardo Collado Torres
★ 1.1k • written 10.0 years ago by
jessica.hekman
▴ 40
8
votes
31
replies
5.0k
views
derfinder: analyzeChr() breaks on chromosomes > 22
derfinder
10.1 years ago
jessica.hekman
▴ 40
2
votes
3
replies
1.5k
views
derfinder: mergeResults() running for three days and still going...
derfinder
10.1 years ago
jessica.hekman
▴ 40
5
votes
20
replies
3.6k
views
derfinder: fullCoverage() problems
derfinder
updated 10.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 10.2 years ago by
jessica.hekman
▴ 40
0
votes
6
replies
2.1k
views
derfinder and BAM indexes
derfinder
10.2 years ago
jessica.hekman
▴ 40
23 results • Page
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Recent ...
Replies
Comment: Error in get_anno_data(ontology) : ontology not supported yet...
by
GODseeker
• 0
thank u so much ,god bless u,my dear friend.
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi @gordonsmyth and @weishi, Firstly, thank you for offering your time to develop the junction quantification module further. This is gre…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
xiaofeiwang198266
• 0
Hi Tim, Thanks for your reply! Yes, my data is 450K, and it is TCGA methylation data downloaded by TCGAbiolinks. The problem is that I can …
Answer: Error in get_anno_data(ontology) : ontology not supported yet...
by
Guido Hooiveld
★ 4.1k
Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…
Comment: Build error on kunpeng2 Linux aarch64
by
martin.grigorov
▴ 10
Hi, There was a problem with `icu` and because of that the (r)curl library was not installed. The system/OS curl library is one version ol…
Votes
Comment: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Comment: Can we get beta values with DMRcate package
Answer: Can we get beta values with DMRcate package
DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
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