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derfinder
•
reset
3
votes
2
replies
1.2k
views
DESeq2 normalization when using with derfinder
Normalization
DESeq2
derfinder
3.2 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 5.3 years ago by
Leonardo Collado Torres
★ 1.1k • written 5.3 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 7.1 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.1 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
2.8k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder
genomicfeatures
genomicranges
updated 7.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.4 years ago by
fruce_ki
▴ 20
2
votes
1
reply
1.4k
views
Read normalization in derfinder
derfinder
normalization
rnaseq
updated 7.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.4 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 7.8 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.8 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
8.1 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 • updated 9.5 years ago
drramki.chop
• 0
0
votes
1
reply
1.6k
views
derfinder fails on findRegions step
derfinder
updated 9.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 9.6 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 9.8 years ago by
jessica.hekman
▴ 40
0
votes
1
reply
1.8k
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
3.6k
views
derfinder: fullCoverage() problems
derfinder
updated 10.2 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
1 of 1
Recent ...
Replies
Answer: Curiously shaped volcano plot with using oarfish + swish to do differential gene
by
Michael Love
43k
See swish vignette, these are explained.
Comment: Problems with oarfish + tximport + swish
by
Michael Love
43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish
by
brown.annaleigh
• 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal
by
iqratechnology4
• 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
by
James W. MacDonald
67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
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Gordon Smyth
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Bob
▴ 10
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shepherl
4.1k
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James W. MacDonald
67k
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Assa Yeroslaviz
★ 1.5k
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