Showing : msa • reset
0
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2
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3.7k
views
Error in msaFun Cannot open input file. No alignment!
msa
written 22 months ago by ▴ 30
0
votes
1
reply
906
views
Cant post a bug report
msa
updated 24 months ago by ▴ 50 • written 2.4 years ago by • 0
0
votes
0
replies
692
views
msa package Error in .local(x, ...) : consensus matrix 'x' is not in proper format
msa
2.5 years ago Yang • 0
0
votes
2
replies
1.2k
views
msa Installation failed - please help
Install msa
2.6 years ago Ido • 0
1
vote
7
replies
5.0k
views
MSA package fails to be installed - installation of package ‘msa’ had non-zero exit status
msa MultipleSequenceAlignment
updated 2.8 years ago by • 0 • written 4.8 years ago by • 0
0
votes
0
replies
659
views
msa module crash
msa
3.0 years ago systems • 0
0
votes
0
replies
1.0k
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
3.0 years ago Mario Dejung • 0
0
votes
7
replies
4.4k
views
msa: object 'msaClustalW' of mode 'function' was not found
msa
updated 3.1 years ago by ▴ 300 • written 5.4 years ago by • 0
0
votes
1
reply
1.3k
views
Error installing package msa on macOS Monterey 12.6 arm64
msa arm64
3.2 years ago lisa.a.ouellette • 0
0
votes
0
replies
1.2k
views
Edit alignment in msa
alig msa Alignment
3.3 years ago Luis • 0
0
votes
1
reply
1.8k
views
Difficulty with msaConvert function in R package
ape msa
updated 3.8 years ago by ▴ 300 • written 4.1 years ago by • 0
1
vote
1
reply
2.6k
views
Msa package clustal-omega
msa
updated 4.1 years ago by ▴ 180 • written 4.1 years ago by • 0
0
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0
replies
1.0k
views
Can I quantify the number of mismatches post alignment?
msa
4.2 years ago Field -Ye • 0
8
votes
8
replies
3.9k
views
msa compilation failure - multiple definition of `GC_jmp_buf' in gc-7.2
software error msa
updated 4.2 years ago by ▴ 300 • written 5.5 years ago by ▴ 40
0
votes
1
reply
1.7k
views
msaprettyprint
msa prettyprint
updated 4.6 years ago by ▴ 300 • written 4.7 years ago by • 0
2
votes
3
replies
3.8k
views
msaprettyprint error in R
msa
updated 5.1 years ago by ▴ 300 • written 5.4 years ago by • 0
0
votes
0
replies
829
views
[Function Request]converts a AA-based fasta alignment (that includes aa fasta sequences of different strains) into a vcf file
msa
5.2 years ago yeli7068 • 0
0
votes
3
replies
2.6k
views
DECIPHER save alignement in outputs
msa decipher output prettyPrint
updated 5.3 years ago by ▴ 300 • written 5.3 years ago by • 0
0
votes
0
replies
1.2k
views
msa: cannot load library silently
msa
5.4 years ago richel • 0
0
votes
3
replies
2.0k
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 5.7 years ago by ▴ 300 • written 5.7 years ago by ▴ 80
1
vote
1
reply
1.9k
views
Error using r msa::msaClustalW in parallel
software error msa
updated 5.9 years ago by ▴ 300 • written 6.0 years ago by ▴ 10
0
votes
1
reply
3.2k
views
Seeking help deploying Shiny application to RStudio Connect with Bioconductor package
Rstudio Connect msa bios2mds BiocManager Bioconductor
6.6 years ago morlenrp • 0
0
votes
1
reply
1.6k
views
Can any of the existing `MSA` packages be used/adapted to visualize a pre-aligned fasta or tsv file (e.g., `kalign` output)?
msa phylogeny
updated 6.7 years ago by ▴ 20 • written 6.7 years ago by • 0
1
vote
2
replies
1.8k
views
What is the '?' in the result of R package 'msa' function 'msa'?
MSA R Multiple sequence alignment consensus sequence
updated 6.7 years ago by ▴ 20 • written 6.7 years ago by • 0
0
votes
9
replies
2.9k
views
visualizing alignment without realignment
msa alignment visualization
updated 6.9 years ago by 25k • written 6.9 years ago by • 0
1
vote
2
replies
2.0k
views
Package for custom visualization of multiple sequence alignment
MSA visualization
updated 7.2 years ago by ▴ 20 • written 7.2 years ago by • 0
0
votes
4
replies
1.8k
views
Error: could not find function "msaConvert"
msa
updated 7.5 years ago by ▴ 300 • written 7.5 years ago by • 0
0
votes
1
reply
1.2k
views
Defining populations in a msaClustalOmega alignment
msa
7.6 years ago cav3gh • 0
2
votes
2
replies
4.9k
views
How to get msa output in fasta format
msa msaprettyprint()
updated 7.7 years ago by ▴ 300 • written 7.7 years ago by • 0
2
votes
2
replies
1.7k
views
seqfault wiht msa
msa segfault
7.7 years ago jmh5ad ▴ 40
0
votes
1
reply
1.9k
views
Status 1 error when using msaPrettyPrint() to make pdfs with MsaAAMultipleAlignment
msaprettyprint() latex pdf msa
updated 8.0 years ago by ▴ 300 • written 8.0 years ago by • 0
0
votes
1
reply
1.8k
views
Error in .Primitive("c")(<S4 object of class "IRanges">) : could not find symbol "recursive" in environment of the generic function running msa
msa iranges
updated 8.0 years ago by ▴ 300 • written 8.0 years ago by • 0
2
votes
11
replies
7.6k
views
How do I extract the complete MsaAAMultipleAlignment object to a file
msaprettyprint() msa multiplealignment export
updated 8.0 years ago by ▴ 300 • written 8.0 years ago by ★ 1.5k
2
votes
4
replies
2.9k
views
running msa (msa) aborts R session
msa alignment r software error
written 8.1 years ago by • 0
3
votes
2
replies
2.8k
views
Installation of MSA package fails
MSA package installation software error compilation error
updated 8.1 years ago by ▴ 300 • written 8.1 years ago by ▴ 10
2
votes
2
replies
3.6k
views
msa: How to obtain a subset of an alignment
msa Biostrings MultipleAlignment
updated 8.3 years ago by ▴ 300 • written 8.3 years ago by ▴ 10
4
votes
5
replies
2.5k
views
Can't install msa on FreeBSD
software error FreeBSD msa
8.4 years ago spcohen2 ▴ 20
1
vote
2
replies
1.8k
views
untranslate AAstringset {Biostrings} or MsaAAMultipleAlignment {msa}
biostrings msa
8.4 years ago multipleseqs • 0
8
votes
14
replies
13k
views
Using msa msaPrettyPrint(): saving multiple alignement fasta file
msa msaprettyprint() fasta
updated 8.6 years ago by • 0 • written 9.0 years ago by ▴ 50
2
votes
5
replies
2.7k
views
Multiple Sequence Alignment using DNA sequence
msa decipher
8.6 years ago bbista91 ▴ 10
2
votes
2
replies
2.5k
views
Error with MSA package - could not find symbol "recursive"
msa
updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 10
2
votes
1
reply
1.9k
views
Outputting a multiple alignment to file error: could not find function write.XStringSet
msa
updated 8.9 years ago by ▴ 300 • written 8.9 years ago by ▴ 10
1
vote
2
replies
1.8k
views
msaPrettyPrint cannot handle long sequences?
msa msaprettyprint() multiple sequence alignment
8.9 years ago map2085 ▴ 40
9
votes
14
replies
4.7k
views
msa package installation problem
msa
updated 8.9 years ago by ▴ 10 • written 9.0 years ago by ▴ 120
2
votes
9
replies
4.8k
views
msa alignement: sorted sequences by sequence name
msa alignement output sorted
9.0 years ago Olorin ▴ 50
1
vote
1
reply
5.7k
views
Using msa msaPrettyPrint(): issues with latex
msa latex msaPrettyPrint()
9.0 years ago Olorin ▴ 50
0
votes
0
replies
1.7k
views
Using readAAMultipleAlignment to parse CMFinder Stockholm format alignments
biostrings stockholm msa cmfinder
9.0 years ago Keith Hughitt ▴ 180
0
votes
1
reply
1.4k
views
How to draw phylogeny tree for long genomes? ('msa' taking much time)
msa phylogenetic
updated 9.1 years ago by ▴ 300 • written 9.1 years ago by ▴ 50
0
votes
1
reply
2.2k
views
Error: could not find function "msaConvert"
msa software error
updated 9.2 years ago by ▴ 300 • written 9.2 years ago by • 0
0
votes
3
replies
2.2k
views
installation failed when trying msa
msa
updated 9.3 years ago by ▴ 300 • written 9.3 years ago by • 0
51 results • Page 1 of 2
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Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 20
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
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Commentator to James W. MacDonald 68k
Great Question to fl ▴ 20
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to Gordon Smyth 53k
Popular Question to Aleena_Ensembl ▴ 30
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