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derfinder
•
reset
3
votes
2
replies
956
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
1000
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 9.1 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
9.4 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
1 of 1
Recent ...
Replies
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
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
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