Showing : MSA • reset
0
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2
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3.5k
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Error in msaFun Cannot open input file. No alignment!
msa
written 21 months ago by ▴ 30
0
votes
1
reply
884
views
Cant post a bug report
msa
updated 23 months ago by ▴ 50 • written 2.3 years ago by • 0
0
votes
0
replies
652
views
msa package Error in .local(x, ...) : consensus matrix 'x' is not in proper format
msa
2.4 years ago Yang • 0
0
votes
2
replies
1.2k
views
msa Installation failed - please help
Install msa
2.5 years ago Ido • 0
1
vote
7
replies
4.9k
views
MSA package fails to be installed - installation of package ‘msa’ had non-zero exit status
msa MultipleSequenceAlignment
updated 2.7 years ago by • 0 • written 4.7 years ago by • 0
0
votes
0
replies
636
views
msa module crash
msa
2.9 years ago systems • 0
0
votes
0
replies
973
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
2.9 years ago Mario Dejung • 0
0
votes
7
replies
4.3k
views
msa: object 'msaClustalW' of mode 'function' was not found
msa
updated 3.0 years ago by ▴ 300 • written 5.3 years ago by • 0
0
votes
1
reply
1.2k
views
Error installing package msa on macOS Monterey 12.6 arm64
msa arm64
3.1 years ago lisa.a.ouellette • 0
0
votes
0
replies
1.2k
views
Edit alignment in msa
alig msa Alignment
3.2 years ago Luis • 0
0
votes
1
reply
1.8k
views
Difficulty with msaConvert function in R package
ape msa
updated 3.7 years ago by ▴ 300 • written 4.0 years ago by • 0
1
vote
1
reply
2.5k
views
Msa package clustal-omega
msa
updated 4.0 years ago by ▴ 180 • written 4.0 years ago by • 0
0
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0
replies
1.0k
views
Can I quantify the number of mismatches post alignment?
msa
4.1 years ago Field -Ye • 0
8
votes
8
replies
3.8k
views
msa compilation failure - multiple definition of `GC_jmp_buf' in gc-7.2
software error msa
updated 4.1 years ago by ▴ 300 • written 5.4 years ago by ▴ 40
0
votes
1
reply
1.7k
views
msaprettyprint
msa prettyprint
updated 4.5 years ago by ▴ 300 • written 4.6 years ago by • 0
2
votes
3
replies
3.7k
views
msaprettyprint error in R
msa
updated 5.0 years ago by ▴ 300 • written 5.3 years ago by • 0
0
votes
0
replies
811
views
[Function Request]converts a AA-based fasta alignment (that includes aa fasta sequences of different strains) into a vcf file
msa
5.1 years ago yeli7068 • 0
0
votes
3
replies
2.5k
views
DECIPHER save alignement in outputs
msa decipher output prettyPrint
updated 5.2 years ago by ▴ 300 • written 5.2 years ago by • 0
0
votes
0
replies
1.1k
views
msa: cannot load library silently
msa
5.3 years ago richel • 0
0
votes
3
replies
1.9k
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 5.6 years ago by ▴ 300 • written 5.6 years ago by ▴ 80
1
vote
1
reply
1.8k
views
Error using r msa::msaClustalW in parallel
software error msa
updated 5.9 years ago by ▴ 300 • written 5.9 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
6.5 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 6.6 years ago by ▴ 20 • written 6.6 years ago by • 0
1
vote
2
replies
1.7k
views
What is the '?' in the result of R package 'msa' function 'msa'?
MSA R Multiple sequence alignment consensus sequence
updated 6.6 years ago by ▴ 20 • written 6.6 years ago by • 0
0
votes
9
replies
2.8k
views
visualizing alignment without realignment
msa alignment visualization
updated 6.8 years ago by 25k • written 6.8 years ago by • 0
1
vote
2
replies
1.9k
views
Package for custom visualization of multiple sequence alignment
MSA visualization
updated 7.1 years ago by ▴ 20 • written 7.1 years ago by • 0
0
votes
4
replies
1.8k
views
Error: could not find function "msaConvert"
msa
updated 7.4 years ago by ▴ 300 • written 7.4 years ago by • 0
0
votes
1
reply
1.2k
views
Defining populations in a msaClustalOmega alignment
msa
7.5 years ago cav3gh • 0
2
votes
2
replies
4.8k
views
How to get msa output in fasta format
msa msaprettyprint()
updated 7.6 years ago by ▴ 300 • written 7.6 years ago by • 0
2
votes
2
replies
1.7k
views
seqfault wiht msa
msa segfault
7.6 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 7.9 years ago by ▴ 300 • written 7.9 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 7.9 years ago by ▴ 300 • written 7.9 years ago by • 0
2
votes
11
replies
7.4k
views
How do I extract the complete MsaAAMultipleAlignment object to a file
msaprettyprint() msa multiplealignment export
updated 7.9 years ago by ▴ 300 • written 7.9 years ago by ★ 1.5k
2
votes
4
replies
2.9k
views
running msa (msa) aborts R session
msa alignment r software error
written 8.0 years ago by • 0
3
votes
2
replies
2.7k
views
Installation of MSA package fails
MSA package installation software error compilation error
updated 8.0 years ago by ▴ 300 • written 8.0 years ago by ▴ 10
2
votes
2
replies
3.6k
views
msa: How to obtain a subset of an alignment
msa Biostrings MultipleAlignment
updated 8.2 years ago by ▴ 300 • written 8.2 years ago by ▴ 10
4
votes
5
replies
2.4k
views
Can't install msa on FreeBSD
software error FreeBSD msa
8.3 years ago spcohen2 ▴ 20
1
vote
2
replies
1.7k
views
untranslate AAstringset {Biostrings} or MsaAAMultipleAlignment {msa}
biostrings msa
8.3 years ago multipleseqs • 0
8
votes
14
replies
12k
views
Using msa msaPrettyPrint(): saving multiple alignement fasta file
msa msaprettyprint() fasta
updated 8.5 years ago by • 0 • written 8.9 years ago by ▴ 50
2
votes
5
replies
2.6k
views
Multiple Sequence Alignment using DNA sequence
msa decipher
8.6 years ago bbista91 ▴ 10
2
votes
2
replies
2.4k
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 8.8 years ago by ▴ 300 • written 8.8 years ago by ▴ 10
1
vote
2
replies
1.8k
views
msaPrettyPrint cannot handle long sequences?
msa msaprettyprint() multiple sequence alignment
8.8 years ago map2085 ▴ 40
9
votes
14
replies
4.6k
views
msa package installation problem
msa
updated 8.8 years ago by ▴ 10 • written 8.9 years ago by ▴ 120
2
votes
9
replies
4.6k
views
msa alignement: sorted sequences by sequence name
msa alignement output sorted
8.9 years ago Olorin ▴ 50
1
vote
1
reply
5.6k
views
Using msa msaPrettyPrint(): issues with latex
msa latex msaPrettyPrint()
8.9 years ago Olorin ▴ 50
0
votes
0
replies
1.6k
views
Using readAAMultipleAlignment to parse CMFinder Stockholm format alignments
biostrings stockholm msa cmfinder
8.9 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 9.0 years ago by ▴ 300 • written 9.0 years ago by ▴ 50
0
votes
1
reply
2.1k
views
Error: could not find function "msaConvert"
msa software error
updated 9.1 years ago by ▴ 300 • written 9.1 years ago by • 0
0
votes
3
replies
2.1k
views
installation failed when trying msa
msa
updated 9.2 years ago by ▴ 300 • written 9.2 years ago by • 0
51 results • Page 1 of 2
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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