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derfinder
•
reset
3
votes
2
replies
857
views
DESeq2 normalization when using with derfinder
Normalization
DESeq2
derfinder
2.1 years ago
Debayan
▴ 20
4
votes
4
replies
985
views
derfinder model.matrix with limma or single base-level F-statistics analysis
derfinder
2.4 years ago
Konstantinos Yeles
▴ 80
3
votes
5
replies
1.1k
views
Detection of large regions of expression
derfinder
intergenic expression
updated 4.2 years ago by
Leonardo Collado Torres
★ 1.0k • written 4.2 years ago by
António Miguel de Jesus Domingues
▴ 490
3
votes
3
replies
1.5k
views
derfinder: how to merge regions and counts from individual chromosomes
derfinder
recount
updated 6.0 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.0 years ago by
António Miguel de Jesus Domingues
▴ 490
2
votes
1
reply
1.2k
views
derfinder mean Expressed Region cutoff
derfinder
updated 6.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.1 years ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
3
replies
1.1k
views
How to preserve the strand of coverage in derfinder::regionMatrix() ?
derfinder
updated 6.3 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.3 years ago by
fruce_ki
▴ 20
3
votes
13
replies
2.1k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder
genomicfeatures
genomicranges
updated 6.3 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.3 years ago by
fruce_ki
▴ 20
2
votes
1
reply
1.1k
views
Read normalization in derfinder
derfinder
normalization
rnaseq
updated 6.3 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.3 years ago by
helene.gylling
▴ 10
2
votes
1
reply
943
views
Derinder options (species, annotations style)
derfinder
rnaseq
differential expression
updated 6.4 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.4 years ago by
fruce_ki
▴ 20
0
votes
1
reply
1.1k
views
derfinder fullCoverage() changes chromosome style and then regionMatrix() complains and ignores provided 'currentStyle'
derfinder
6.6 years ago
Wayne
• 0
0
votes
7
replies
1.8k
views
regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder
GenomeInfoDb
GenomicRanges
6.6 years ago
Wayne
• 0
0
votes
1
reply
1.6k
views
error with base-level DERfinder using large sample sizes
derfinder
updated 6.7 years ago by
Leonardo Collado Torres
★ 1.0k • written 6.7 years ago by
andrewelamb
• 0
1
vote
10
replies
3.1k
views
Issue creating a genomic state object in derfinder from an Ensembl GTF file
derfinder
genomicfeatures
6.8 years ago
Leonardo Collado Torres
★ 1.0k
1
vote
2
replies
1.1k
views
derfinder on bacteria PE strand specific RNA-seq
derfinder
7.0 years ago
eva.pinatel
▴ 10
2
votes
6
replies
2.0k
views
derfinder gets stuck in calculatePvalues
derfinder
software error
rnaseq
8.5 years ago • updated 8.4 years ago
drramki.chop
• 0
0
votes
1
reply
1.3k
views
derfinder fails on findRegions step
derfinder
updated 8.5 years ago by
Leonardo Collado Torres
★ 1.0k • written 8.5 years ago by
pschaugh
• 0
9
votes
20
replies
2.4k
views
derfinder: analyzeChr() freezes in f-stat calculation
derfinder
updated 8.7 years ago by
Leonardo Collado Torres
★ 1.0k • written 8.7 years ago by
jessica.hekman
▴ 40
0
votes
1
reply
1.5k
views
Error message suggestion for fullCoverage in derfinder
derfinder
updated 8.8 years ago by
Leonardo Collado Torres
★ 1.0k • written 8.9 years ago by
jessica.hekman
▴ 40
1
vote
10
replies
2.1k
views
derfinder failing in mergeResults()
derfinder
updated 8.8 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.0 years ago by
jessica.hekman
▴ 40
8
votes
31
replies
3.9k
views
derfinder: analyzeChr() breaks on chromosomes > 22
derfinder
9.1 years ago
jessica.hekman
▴ 40
2
votes
3
replies
1.2k
views
derfinder: mergeResults() running for three days and still going...
derfinder
9.1 years ago
jessica.hekman
▴ 40
5
votes
20
replies
2.7k
views
derfinder: fullCoverage() problems
derfinder
updated 9.1 years ago by
Leonardo Collado Torres
★ 1.0k • written 9.1 years ago by
jessica.hekman
▴ 40
0
votes
6
replies
1.8k
views
derfinder and BAM indexes
derfinder
9.2 years ago
jessica.hekman
▴ 40
23 results • Page
1 of 1
Recent ...
Replies
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
ATpoint
★ 3.6k
"Raw" counts, so you're plotting un-normalized data, hence plots have no meaning in terms of groupwise comparisons. Use the `normTransform`…
Answer: In DiffBind, dba.blacklist changes the minOverlap parameter
by
Sam
▴ 10
I have found a workaround : running dba.blacklist **after** running dba.count (while running dba.count with minOverlap=1). ``` dbObj_co…
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
samer
• 0
By applying the log2 transformation to the raw counts of small RNAS AND after adding 1 to each count, the resulting values often approximat…
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
samer
• 0
and sometimes in other count plots we observe a difference between the counts of the 2 conditions (ON/OFF) where it should be significant b…
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
ATpoint
★ 3.6k
What is `Log2 Counts + 1`? Please show code for the plots. And please remove the comments and move everything to the toplevel question usin…
Votes
Answer: WGCNA documentation not available
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Answer: Correct the batch effect in methylation analysis in R
Comment: Why is DMRcate not available for Bioconductor version 3.18?
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