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derfinder
•
reset
3
votes
2
replies
988
views
DESeq2 normalization when using with derfinder
Normalization
DESeq2
derfinder
2.6 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
Konstantinos Yeles
▴ 80
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
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
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
0
votes
3
replies
1.3k
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
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 6.8 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
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
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
2.1k
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 7.2 years ago by
Leonardo Collado Torres
★ 1.0k • written 7.2 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
7.5 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
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 9.0 years ago by
pschaugh
• 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 9.2 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
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
8
votes
31
replies
4.4k
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 9.6 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.6 years ago by
jessica.hekman
▴ 40
0
votes
6
replies
1.9k
views
derfinder and BAM indexes
derfinder
9.6 years ago
jessica.hekman
▴ 40
23 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters
by
anne-laure
• 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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Vincent J. Carey, Jr.
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Koen Van den Berge
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3.9k
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