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pairwisealignment
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637
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Question about converting SAM alignment file data to a visual text alignment (e.g., resembling blastn alignment)
SAM
samtools
pairwisealignment
alignment
blastn
4.5 years ago
ktehmsen
• 0
0
votes
3
replies
806
views
How to find multiple overlaps with pairwiseAlignment()?
biostrings
pairwisealignment
updated 5.0 years ago by
Hervé Pagès
16k • written 5.0 years ago by
kgorczak
▴ 10
0
votes
4
replies
726
views
Query with Biostrings pairwise alignment output positon
biostrings
alignment
pairwisealignment
updated 5.1 years ago by
Hervé Pagès
16k • written 5.1 years ago by
dhwani2410
• 0
1
vote
2
replies
2.7k
views
Calculate the number of SNP differences between sequences in multiple alignment
pairwisealignment
SNP
dnasequence
6.0 years ago
lordbleys
• 0
0
votes
0
replies
672
views
Translate to aminoacid, align pairwise and un-translate back to DNA
translation
pairwisealignment
6.5 years ago
igferres
• 0
0
votes
1
reply
610
views
Mapping sequence features to alignments
pairwisealignment
indel
updated 6.6 years ago by
Hervé Pagès
16k • written 6.6 years ago by
oliwindram
▴ 10
3
votes
2
replies
945
views
pairwiseAlignments coordinate mapping?
biostrings
pairwisealignment
updated 6.7 years ago by
Hervé Pagès
16k • written 6.7 years ago by
Steve Lianoglou
13k
2
votes
1
reply
760
views
Error in score() function on pairwiseAlignment()
biostrings
pairwisealignment
updated 6.7 years ago by
shepherl
3.4k • written 6.7 years ago by
jdydu
• 0
0
votes
1
reply
964
views
pairwiseAlignment() - Similarity NA% ?
biostrings
pairwisealignment
updated 7.3 years ago by
Hervé Pagès
16k • written 7.3 years ago by
boris.steipe
• 0
2
votes
3
replies
880
views
indels located at the edges of subject and Biostrings pairwiseAlignment function
pairwisealignment
biostrings
7.3 years ago
vincent.plagnol
▴ 10
0
votes
2
replies
1.3k
views
inconsistent pairwiseAlignment behaviour (Biostrings) with multiple alignments with identical scores
biostrings
pairwisealignment
7.4 years ago
vincent.plagnol
▴ 10
4
votes
5
replies
2.0k
views
global alignment in Biostrings , Memory fails when seq. lengths around 50K bp
Biostrings
pairwiseAlignment
updated 8.2 years ago by
Hervé Pagès
16k • written 8.2 years ago by
branislav misovic
▴ 120
12 results • Page
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Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
by
Hervé Pagès
16k
See https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
by
Hervé Pagès
16k
See https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932
Comment: Sva and batch effect
by
Gordon Smyth
47k
(+1). I find that ComBat tends to introduce spurious differential expression so, you think there's a batch effect affecting the variances a…
Comment: Advice for the analysis of microarray data with limma
by
Gordon Smyth
47k
You mean references on orthogonal polynomials? Polynomial approximation is a classic topic in mathematics and statistics and there are many…
Comment: Limma-voom with inverse probability weights (similar to sample weights)
by
Gordon Smyth
47k
The potential problem isn't with empirical Bayes with the fact that the variance estimate from your method A linear model might not be mean…
Votes
Answer: Sva and batch effect
Answer: AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Answer: Limma-voom with inverse probability weights
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