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derfinder
•
reset
3
votes
2
replies
314
views
DESeq2 normalization when using with derfinder
Normalization
DESeq2
derfinder
7 months ago
Debayan
▴ 20
4
votes
4
replies
431
views
derfinder model.matrix with limma or single base-level F-statistics analysis
derfinder
10 months ago • updated 9 months ago
Konstantinos Yeles
▴ 70
3
votes
5
replies
565
views
Detection of large regions of expression
derfinder
intergenic expression
updated 2.7 years ago by
Leonardo Collado Torres
▴ 980 • written 2.7 years ago by
António Miguel de Jesus Domingues
▴ 480
3
votes
3
replies
1.0k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder
recount
updated 4.5 years ago by
Leonardo Collado Torres
▴ 980 • written 4.5 years ago by
António Miguel de Jesus Domingues
▴ 480
2
votes
1
reply
780
views
derfinder mean Expressed Region cutoff
derfinder
updated 4.5 years ago by
Leonardo Collado Torres
▴ 980 • written 4.5 years ago by
António Miguel de Jesus Domingues
▴ 480
0
votes
3
replies
719
views
How to preserve the strand of coverage in derfinder::regionMatrix() ?
derfinder
updated 4.7 years ago by
Leonardo Collado Torres
▴ 980 • written 4.7 years ago by
fruce_ki
▴ 20
3
votes
13
replies
1.4k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder
genomicfeatures
genomicranges
updated 4.8 years ago by
Leonardo Collado Torres
▴ 980 • written 4.8 years ago by
fruce_ki
▴ 20
2
votes
1
reply
817
views
Read normalization in derfinder
derfinder
normalization
rnaseq
updated 4.8 years ago by
Leonardo Collado Torres
▴ 980 • written 4.8 years ago by
helene.gylling
▴ 10
2
votes
1
reply
698
views
Derinder options (species, annotations style)
derfinder
rnaseq
differential expression
updated 4.8 years ago by
Leonardo Collado Torres
▴ 980 • written 4.8 years ago by
fruce_ki
▴ 20
0
votes
1
reply
798
views
derfinder fullCoverage() changes chromosome style and then regionMatrix() complains and ignores provided 'currentStyle'
derfinder
5.1 years ago
Wayne
• 0
0
votes
7
replies
1.2k
views
regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder
GenomeInfoDb
GenomicRanges
5.1 years ago
Wayne
• 0
0
votes
1
reply
1.3k
views
error with base-level DERfinder using large sample sizes
derfinder
updated 5.2 years ago by
Leonardo Collado Torres
▴ 980 • written 5.2 years ago by
andrewelamb
• 0
1
vote
10
replies
2.4k
views
Issue creating a genomic state object in derfinder from an Ensembl GTF file
derfinder
genomicfeatures
5.2 years ago
Leonardo Collado Torres
▴ 980
1
vote
2
replies
805
views
derfinder on bacteria PE strand specific RNA-seq
derfinder
5.5 years ago
eva.pinatel
▴ 10
2
votes
6
replies
1.6k
views
derfinder gets stuck in calculatePvalues
derfinder
software error
rnaseq
7.0 years ago • updated 6.9 years ago
drramki.chop
• 0
0
votes
1
reply
1.1k
views
derfinder fails on findRegions step
derfinder
updated 7.0 years ago by
Leonardo Collado Torres
▴ 980 • written 7.0 years ago by
pschaugh
• 0
9
votes
20
replies
1.7k
views
derfinder: analyzeChr() freezes in f-stat calculation
derfinder
updated 7.1 years ago by
Leonardo Collado Torres
▴ 980 • written 7.2 years ago by
jessica.hekman
▴ 40
0
votes
1
reply
1.2k
views
Error message suggestion for fullCoverage in derfinder
derfinder
updated 7.2 years ago by
Leonardo Collado Torres
▴ 980 • written 7.3 years ago by
jessica.hekman
▴ 40
1
vote
10
replies
1.6k
views
derfinder failing in mergeResults()
derfinder
updated 7.2 years ago by
Leonardo Collado Torres
▴ 980 • written 7.4 years ago by
jessica.hekman
▴ 40
8
votes
31
replies
2.7k
views
derfinder: analyzeChr() breaks on chromosomes > 22
derfinder
7.6 years ago
jessica.hekman
▴ 40
2
votes
3
replies
888
views
derfinder: mergeResults() running for three days and still going...
derfinder
7.6 years ago
jessica.hekman
▴ 40
5
votes
20
replies
1.8k
views
derfinder: fullCoverage() problems
derfinder
updated 7.6 years ago by
Leonardo Collado Torres
▴ 980 • written 7.6 years ago by
jessica.hekman
▴ 40
0
votes
6
replies
1.2k
views
derfinder and BAM indexes
derfinder
7.6 years ago
jessica.hekman
▴ 40
23 results • Page
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Recent ...
Replies
Comment: Italicise
by
Kevin Blighe
3.5k
Okay, I am guessing that the problem is that you need to update the version of *EnhancedVolcano* to the latest version. Can you try that? T…
Comment: Italicise
by
Pau
• 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa
by
priyanka.m
• 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
by
wahaha
• 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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