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PWMEnrich
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0
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762
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How to interpret difference statistic from the output of the motifDiffEnrichment() function in the PWMEnrich package?
PWMEnrich
6.0 years ago
intregen
• 0
0
votes
0
replies
892
views
makeBackground error message "Sequence only contain N's"
pwmenrich
6.7 years ago
gdeniz
• 0
0
votes
1
reply
975
views
subsetting PWMLognBackground object in the PWMEnrich package
PWMEnrich
6.8 years ago
amanda.joy.price
▴ 10
0
votes
0
replies
811
views
PWMEnruch: Error in getPromoters(organism)
r
pwmenrich
6.9 years ago
prp291
• 0
0
votes
1
reply
2.1k
views
Convert HOMER motif matrix to pfm?
homer
pwmenrich
updated 8.3 years ago by
Ou, Jianhong
★ 1.3k • written 8.3 years ago by
sarah.blackstone7734
• 0
0
votes
0
replies
1.1k
views
question about motif enrichment analysis using PWMenrich
PWMenrich
8.4 years ago
sekawaiwai2006
▴ 20
2
votes
3
replies
2.0k
views
visualing pwm motif on a DNAstring
pwmenrich
dnastringset
updated 8.8 years ago by
Robert Stojnic
▴ 50 • written 8.8 years ago by
sekawaiwai2006
▴ 20
0
votes
0
replies
1.5k
views
Import motifs in .meme format in MotifDB
motfdb
pwmenrich
meme
8.8 years ago
enricoferrero
▴ 660
0
votes
3
replies
1.6k
views
motif scanning using position frequncy matrix of motif in a given set of DNAstringset sequnces?.
motifdb
matchpwm
motif
pwmenrich
pwm
9.1 years ago
vinod.acear
▴ 50
0
votes
1
reply
2.4k
views
non-numeric argument to binary operator error with makeBackground() in PWMEnrich
pwmenrich
MotifDB
updated 9.2 years ago by
Robert Stojnic
▴ 50 • written 9.2 years ago by
elliott77
• 0
2
votes
1
reply
1.2k
views
[PWMEnrich] Enrichment p-values on human sequences
pwmenrich
log
updated 9.4 years ago by
Robert Stojnic
▴ 50 • written 9.4 years ago by
enricoferrero
▴ 660
1
vote
3
replies
1.6k
views
getBackgroundFrequencies for Arabidopsis
pwmenrich
bsgenome
9.4 years ago
oliwindram
▴ 10
0
votes
5
replies
2.8k
views
Motif enrichment analysis: Error in transfac format and background frequencies from BSGenome
BSgenome
convert
BSgenome
PWMEnrich
MotifDb
updated 10.3 years ago by
Robert Stojnic
▴ 80 • written 10.3 years ago by
deepti anand
▴ 50
0
votes
0
replies
897
views
PWMEnrich::sequenceReport() and 'res' global variable
PWMEnrich
PWMEnrich
10.5 years ago
enricoferrero
▴ 660
0
votes
8
replies
1.8k
views
plotpfm has been removed in PWMEnrich?
PWMEnrich
PWMEnrich
updated 11.1 years ago by
Robert Stojnic
▴ 80 • written 11.1 years ago by
Fabrice Tourre
▴ 970
0
votes
1
reply
1.4k
views
PWMEnrich binding site position
PWMEnrich
PWMEnrich
updated 11.3 years ago by
Robert Stojnic
▴ 50 • written 11.3 years ago by
Guest User
★ 13k
16 results • Page
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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Gordon Smyth
52k
It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Andre
• 0
Thank you. What is the difference between setting robust=TRUE in glmQLFit and estimateGLMRobustDisp? The paper i mentioned in the post used…
Comment: PCA of different bacterial species
by
Jeremy
• 0
Your approach of using ~2500 single-copy orthologs and normalizing with VST or rlog for PCA is valid for exploring general clustering [pap…
Comment: RnBeads::combine() - error?
by
Urotree
• 0
pheno <- rnb.set.arrays@pheno # Phenotypic data sites <- rnb.set.arrays@sites # CpG site definitions (data.frame) meth <- rnb.set…
Comment: RnBeads::combine() - error?
by
Urotree
• 0
![enter image description here][1] [1]: /media/images/40d9778d-b044-4405-9b3d-2ba835f6 Hi, after I convert to RnBiseqSet, it shows "All…
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Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
scater/scran with TPMs from Salmon - counts?
A: Full length single-cell RNA-seq - tximport output for downstream analysis
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