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PWMenrich
•
reset
0
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0
replies
804
views
How to interpret difference statistic from the output of the motifDiffEnrichment() function in the PWMEnrich package?
PWMEnrich
6.3 years ago
intregen
• 0
0
votes
0
replies
942
views
makeBackground error message "Sequence only contain N's"
pwmenrich
7.0 years ago
gdeniz
• 0
0
votes
1
reply
1.1k
views
subsetting PWMLognBackground object in the PWMEnrich package
PWMEnrich
7.1 years ago
amanda.joy.price
▴ 10
0
votes
0
replies
856
views
PWMEnruch: Error in getPromoters(organism)
r
pwmenrich
7.2 years ago
prp291
• 0
0
votes
1
reply
2.3k
views
Convert HOMER motif matrix to pfm?
homer
pwmenrich
updated 8.6 years ago by
Ou, Jianhong
★ 1.3k • written 8.7 years ago by
sarah.blackstone7734
• 0
0
votes
0
replies
1.2k
views
question about motif enrichment analysis using PWMenrich
PWMenrich
8.7 years ago
sekawaiwai2006
▴ 20
2
votes
3
replies
2.2k
views
visualing pwm motif on a DNAstring
pwmenrich
dnastringset
updated 9.1 years ago by
Robert Stojnic
▴ 50 • written 9.1 years ago by
sekawaiwai2006
▴ 20
0
votes
0
replies
1.5k
views
Import motifs in .meme format in MotifDB
motfdb
pwmenrich
meme
9.1 years ago
enricoferrero
▴ 680
0
votes
3
replies
1.7k
views
motif scanning using position frequncy matrix of motif in a given set of DNAstringset sequnces?.
motifdb
matchpwm
motif
pwmenrich
pwm
9.4 years ago
vinod.acear
▴ 50
0
votes
1
reply
2.5k
views
non-numeric argument to binary operator error with makeBackground() in PWMEnrich
pwmenrich
MotifDB
updated 9.5 years ago by
Robert Stojnic
▴ 50 • written 9.5 years ago by
elliott77
• 0
2
votes
1
reply
1.3k
views
[PWMEnrich] Enrichment p-values on human sequences
pwmenrich
log
updated 9.7 years ago by
Robert Stojnic
▴ 50 • written 9.7 years ago by
enricoferrero
▴ 680
1
vote
3
replies
1.7k
views
getBackgroundFrequencies for Arabidopsis
pwmenrich
bsgenome
9.7 years ago
oliwindram
▴ 10
0
votes
5
replies
2.9k
views
Motif enrichment analysis: Error in transfac format and background frequencies from BSGenome
BSgenome
convert
BSgenome
PWMEnrich
MotifDb
updated 10.6 years ago by
Robert Stojnic
▴ 80 • written 10.6 years ago by
deepti anand
▴ 50
0
votes
0
replies
932
views
PWMEnrich::sequenceReport() and 'res' global variable
PWMEnrich
PWMEnrich
10.8 years ago
enricoferrero
▴ 680
0
votes
8
replies
2.0k
views
plotpfm has been removed in PWMEnrich?
PWMEnrich
PWMEnrich
updated 11.4 years ago by
Robert Stojnic
▴ 80 • written 11.4 years ago by
Fabrice Tourre
▴ 970
0
votes
1
reply
1.4k
views
PWMEnrich binding site position
PWMEnrich
PWMEnrich
updated 11.6 years ago by
Robert Stojnic
▴ 50 • written 11.6 years ago by
Guest User
★ 13k
16 results • Page
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Comment: CluserProfiler message "No gene can be mapped"
by
Carolina
• 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE
by
James W. MacDonald
68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation
by
sergisayolspuig
▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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