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pairwiseAlignment
•
reset
1
vote
2
replies
3.5k
views
Calculate the number of SNP differences between sequences in multiple alignment
pairwisealignment
SNP
dnasequence
7.2 years ago
lordbleys
• 0
4
votes
5
replies
2.6k
views
global alignment in Biostrings , Memory fails when seq. lengths around 50K bp
Biostrings
pairwiseAlignment
updated 9.5 years ago by
Hervé Pagès
16k • written 9.5 years ago by
branislav misovic
▴ 120
0
votes
2
replies
1.6k
views
inconsistent pairwiseAlignment behaviour (Biostrings) with multiple alignments with identical scores
biostrings
pairwisealignment
8.6 years ago
vincent.plagnol
▴ 10
0
votes
3
replies
1.4k
views
How to find multiple overlaps with pairwiseAlignment()?
biostrings
pairwisealignment
updated 6.3 years ago by
Hervé Pagès
16k • written 6.3 years ago by
kgorczak
▴ 10
3
votes
2
replies
1.4k
views
pairwiseAlignments coordinate mapping?
biostrings
pairwisealignment
updated 8.0 years ago by
Hervé Pagès
16k • written 8.0 years ago by
Steve Lianoglou
★ 13k
0
votes
4
replies
1.4k
views
Query with Biostrings pairwise alignment output positon
biostrings
alignment
pairwisealignment
updated 6.4 years ago by
Hervé Pagès
16k • written 6.4 years ago by
dhwani2410
• 0
0
votes
1
reply
1.3k
views
pairwiseAlignment() - Similarity NA% ?
biostrings
pairwisealignment
updated 8.6 years ago by
Hervé Pagès
16k • written 8.6 years ago by
boris.steipe
• 0
2
votes
3
replies
1.2k
views
indels located at the edges of subject and Biostrings pairwiseAlignment function
pairwisealignment
biostrings
8.6 years ago
vincent.plagnol
▴ 10
0
votes
0
replies
1.1k
views
Question about converting SAM alignment file data to a visual text alignment (e.g., resembling blastn alignment)
SAM
samtools
pairwisealignment
alignment
blastn
5.7 years ago
ktehmsen
• 0
2
votes
1
reply
1.0k
views
Error in score() function on pairwiseAlignment()
biostrings
pairwisealignment
updated 8.0 years ago by
shepherl
3.9k • written 8.0 years ago by
jdydu
• 0
0
votes
0
replies
995
views
Translate to aminoacid, align pairwise and un-translate back to DNA
translation
pairwisealignment
7.7 years ago
igferres
• 0
0
votes
1
reply
879
views
Mapping sequence features to alignments
pairwisealignment
indel
updated 7.8 years ago by
Hervé Pagès
16k • written 7.8 years ago by
oliwindram
▴ 10
12 results • Page
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Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
nbay13
• 0
A little late to the party, but I found that using the equation you specified, the p-values are actually slightly off from base R's `t.test…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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