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derfinder
•
reset
3
votes
2
replies
1.2k
views
DESeq2 normalization when using with derfinder
Normalization
DESeq2
derfinder
3.3 years ago
Debayan
▴ 20
4
votes
4
replies
1.4k
views
derfinder model.matrix with limma or single base-level F-statistics analysis
derfinder
3.5 years ago
Konstantinos Yeles
▴ 80
3
votes
5
replies
1.5k
views
Detection of large regions of expression
derfinder
intergenic expression
updated 5.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 5.4 years ago by
António Miguel de Jesus Domingues
▴ 510
3
votes
3
replies
2.1k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder
recount
updated 7.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.2 years ago by
António Miguel de Jesus Domingues
▴ 510
2
votes
1
reply
1.6k
views
derfinder mean Expressed Region cutoff
derfinder
updated 7.2 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.2 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 7.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.4 years ago by
fruce_ki
▴ 20
3
votes
13
replies
2.9k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder
genomicfeatures
genomicranges
updated 7.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.5 years ago by
fruce_ki
▴ 20
2
votes
1
reply
1.4k
views
Read normalization in derfinder
derfinder
normalization
rnaseq
updated 7.5 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.5 years ago by
helene.gylling
▴ 10
2
votes
1
reply
1.2k
views
Derinder options (species, annotations style)
derfinder
rnaseq
differential expression
updated 7.5 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.5 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
7.7 years ago
Wayne
• 0
0
votes
7
replies
2.5k
views
regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder
GenomeInfoDb
GenomicRanges
7.7 years ago
Wayne
• 0
0
votes
1
reply
1.9k
views
error with base-level DERfinder using large sample sizes
derfinder
updated 7.9 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.9 years ago by
andrewelamb
• 0
1
vote
10
replies
3.9k
views
Issue creating a genomic state object in derfinder from an Ensembl GTF file
derfinder
genomicfeatures
7.9 years ago
Leonardo Collado Torres
★ 1.1k
1
vote
2
replies
1.5k
views
derfinder on bacteria PE strand specific RNA-seq
derfinder
8.2 years ago
eva.pinatel
▴ 10
2
votes
6
replies
2.5k
views
derfinder gets stuck in calculatePvalues
derfinder
software error
rnaseq
9.6 years ago
drramki.chop
• 0
0
votes
1
reply
1.6k
views
derfinder fails on findRegions step
derfinder
updated 9.7 years ago by
Leonardo Collado Torres
★ 1.1k • written 9.7 years ago by
pschaugh
• 0
9
votes
20
replies
3.2k
views
derfinder: analyzeChr() freezes in f-stat calculation
derfinder
updated 9.8 years ago by
Leonardo Collado Torres
★ 1.1k • written 9.9 years ago by
jessica.hekman
▴ 40
0
votes
1
reply
1.9k
views
Error message suggestion for fullCoverage in derfinder
derfinder
updated 9.9 years ago by
Leonardo Collado Torres
★ 1.1k • written 10.0 years ago by
jessica.hekman
▴ 40
1
vote
10
replies
2.7k
views
derfinder failing in mergeResults()
derfinder
updated 9.9 years ago by
Leonardo Collado Torres
★ 1.1k • written 10.1 years ago by
jessica.hekman
▴ 40
8
votes
31
replies
5.1k
views
derfinder: analyzeChr() breaks on chromosomes > 22
derfinder
10.2 years ago
jessica.hekman
▴ 40
2
votes
3
replies
1.6k
views
derfinder: mergeResults() running for three days and still going...
derfinder
10.2 years ago
jessica.hekman
▴ 40
5
votes
20
replies
3.7k
views
derfinder: fullCoverage() problems
derfinder
updated 10.3 years ago by
Leonardo Collado Torres
★ 1.1k • written 10.3 years ago by
jessica.hekman
▴ 40
0
votes
6
replies
2.2k
views
derfinder and BAM indexes
derfinder
10.3 years ago
jessica.hekman
▴ 40
23 results • Page
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Comment: Identifying potentially associated gene set to drug response using GSVA
by
kl2023gege
• 0
Thanks for sharing. You gotta check out Sprunki Phase Games on [Sprunki Phase](https://sprunkiphase.net). It's a wild ride of tunes and tw…
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot
by
Quang NN
▴ 10
I see. Thank you ATpoint!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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