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derfinder
•
reset
3
votes
2
replies
969
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
1.3k
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 6.7 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
7.1 years ago
Leonardo Collado Torres
★ 1.0k
1
vote
2
replies
1.2k
views
derfinder on bacteria PE strand specific RNA-seq
derfinder
7.4 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
1.4k
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
2.6k
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 9.2 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 9.3 years ago by
jessica.hekman
▴ 40
8
votes
31
replies
4.3k
views
derfinder: analyzeChr() breaks on chromosomes > 22
derfinder
9.5 years ago • updated 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
3.1k
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
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Recent ...
Replies
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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