Showing : MSA • reset
0
votes
2
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1.7k
views
Error in msaFun Cannot open input file. No alignment!
msa
written 9 months ago by ▴ 30
0
votes
1
reply
612
views
Cant post a bug report
msa
updated 11 months ago by ▴ 50 • written 16 months ago by • 0
0
votes
0
replies
462
views
msa package Error in .local(x, ...) : consensus matrix 'x' is not in proper format
msa
17 months ago Yang • 0
0
votes
2
replies
805
views
msa Installation failed - please help
Install msa
19 months ago Ido • 0
1
vote
7
replies
3.8k
views
MSA package fails to be installed - installation of package ‘msa’ had non-zero exit status
msa MultipleSequenceAlignment
updated 21 months ago by • 0 • written 3.8 years ago by • 0
0
votes
0
replies
490
views
msa module crash
msa
23 months ago systems • 0
0
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0
replies
711
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
23 months ago Mario Dejung • 0
0
votes
7
replies
3.5k
views
msa: object 'msaClustalW' of mode 'function' was not found
msa
updated 2.0 years ago by ▴ 300 • written 4.3 years ago by • 0
0
votes
1
reply
990
views
Error installing package msa on macOS Monterey 12.6 arm64
msa arm64
2.2 years ago lisa.a.ouellette • 0
0
votes
0
replies
915
views
Edit alignment in msa
alig msa Alignment
2.2 years ago Luis • 0
0
votes
1
reply
1.4k
views
Difficulty with msaConvert function in R package
ape msa
updated 2.7 years ago by ▴ 300 • written 3.1 years ago by • 0
1
vote
1
reply
1.7k
views
Msa package clustal-omega
msa
updated 3.0 years ago by ▴ 180 • written 3.0 years ago by • 0
0
votes
0
replies
777
views
Can I quantify the number of mismatches post alignment?
msa
3.1 years ago Field -Ye • 0
8
votes
8
replies
3.1k
views
msa compilation failure - multiple definition of `GC_jmp_buf' in gc-7.2
software error msa
updated 3.2 years ago by ▴ 300 • written 4.5 years ago by ▴ 40
0
votes
1
reply
1.4k
views
msaprettyprint
msa prettyprint
updated 3.6 years ago by ▴ 300 • written 3.6 years ago by • 0
2
votes
3
replies
3.2k
views
msaprettyprint error in R
msa
updated 4.0 years ago by ▴ 300 • written 4.3 years ago by • 0
0
votes
0
replies
658
views
[Function Request]converts a AA-based fasta alignment (that includes aa fasta sequences of different strains) into a vcf file
msa
4.1 years ago yeli7068 • 0
0
votes
3
replies
2.1k
views
DECIPHER save alignement in outputs
msa decipher output prettyPrint
updated 4.3 years ago by ▴ 300 • written 4.3 years ago by • 0
0
votes
0
replies
934
views
msa: cannot load library silently
msa
4.3 years ago richel • 0
0
votes
3
replies
1.6k
views
Align a list of DNA sequence, extract only positions with SNPs for conpact view?
msa Biostrings
updated 4.7 years ago by ▴ 300 • written 4.7 years ago by ▴ 80
1
vote
1
reply
1.5k
views
Error using r msa::msaClustalW in parallel
software error msa
updated 4.9 years ago by ▴ 300 • written 4.9 years ago by ▴ 10
0
votes
1
reply
2.8k
views
Seeking help deploying Shiny application to RStudio Connect with Bioconductor package
Rstudio Connect msa bios2mds BiocManager Bioconductor
5.5 years ago morlenrp • 0
0
votes
1
reply
1.3k
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 5.6 years ago by ▴ 20 • written 5.6 years ago by • 0
1
vote
2
replies
1.3k
views
What is the '?' in the result of R package 'msa' function 'msa'?
MSA R Multiple sequence alignment consensus sequence
updated 5.6 years ago by ▴ 20 • written 5.6 years ago by • 0
0
votes
9
replies
2.3k
views
visualizing alignment without realignment
msa alignment visualization
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
1
vote
2
replies
1.5k
views
Package for custom visualization of multiple sequence alignment
MSA visualization
updated 6.2 years ago by ▴ 20 • written 6.2 years ago by • 0
0
votes
4
replies
1.5k
views
Error: could not find function "msaConvert"
msa
updated 6.5 years ago by ▴ 300 • written 6.5 years ago by • 0
0
votes
1
reply
1.0k
views
Defining populations in a msaClustalOmega alignment
msa
6.5 years ago cav3gh • 0
2
votes
2
replies
4.1k
views
How to get msa output in fasta format
msa msaprettyprint()
updated 6.6 years ago by ▴ 300 • written 6.6 years ago by • 0
2
votes
2
replies
1.3k
views
seqfault wiht msa
msa segfault
6.6 years ago jmh5ad ▴ 40
0
votes
1
reply
1.6k
views
Status 1 error when using msaPrettyPrint() to make pdfs with MsaAAMultipleAlignment
msaprettyprint() latex pdf msa
updated 6.9 years ago by ▴ 300 • written 6.9 years ago by • 0
0
votes
1
reply
1.6k
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 6.9 years ago by ▴ 300 • written 6.9 years ago by • 0
2
votes
11
replies
6.2k
views
How do I extract the complete MsaAAMultipleAlignment object to a file
msaprettyprint() msa multiplealignment export
updated 6.9 years ago by ▴ 300 • written 6.9 years ago by ★ 1.5k
2
votes
4
replies
2.4k
views
running msa (msa) aborts R session
msa alignment r software error
written 7.0 years ago by • 0
3
votes
2
replies
2.2k
views
Installation of MSA package fails
MSA package installation software error compilation error
updated 7.0 years ago by ▴ 300 • written 7.0 years ago by ▴ 10
2
votes
2
replies
2.8k
views
msa: How to obtain a subset of an alignment
msa Biostrings MultipleAlignment
updated 7.3 years ago by ▴ 300 • written 7.3 years ago by ▴ 10
4
votes
5
replies
2.0k
views
Can't install msa on FreeBSD
software error FreeBSD msa
7.3 years ago spcohen2 ▴ 20
1
vote
2
replies
1.4k
views
untranslate AAstringset {Biostrings} or MsaAAMultipleAlignment {msa}
biostrings msa
7.4 years ago multipleseqs • 0
8
votes
14
replies
11k
views
Using msa msaPrettyPrint(): saving multiple alignement fasta file
msa msaprettyprint() fasta
updated 7.6 years ago by • 0 • written 7.9 years ago by ▴ 50
2
votes
5
replies
2.1k
views
Multiple Sequence Alignment using DNA sequence
msa decipher
7.6 years ago bbista91 ▴ 10
2
votes
2
replies
2.2k
views
Error with MSA package - could not find symbol "recursive"
msa
updated 7.8 years ago by 25k • written 7.8 years ago by ▴ 10
2
votes
1
reply
1.6k
views
Outputting a multiple alignment to file error: could not find function write.XStringSet
msa
updated 7.8 years ago by ▴ 300 • written 7.8 years ago by ▴ 10
1
vote
2
replies
1.5k
views
msaPrettyPrint cannot handle long sequences?
msa msaprettyprint() multiple sequence alignment
7.8 years ago map2085 ▴ 40
9
votes
14
replies
3.8k
views
msa package installation problem
msa
updated 7.9 years ago by ▴ 10 • written 8.0 years ago by ▴ 120
2
votes
9
replies
3.8k
views
msa alignement: sorted sequences by sequence name
msa alignement output sorted
7.9 years ago Olorin ▴ 50
1
vote
1
reply
5.2k
views
Using msa msaPrettyPrint(): issues with latex
msa latex msaPrettyPrint()
7.9 years ago Olorin ▴ 50
0
votes
0
replies
1.4k
views
Using readAAMultipleAlignment to parse CMFinder Stockholm format alignments
biostrings stockholm msa cmfinder
8.0 years ago Keith Hughitt ▴ 180
0
votes
1
reply
1.2k
views
How to draw phylogeny tree for long genomes? ('msa' taking much time)
msa phylogenetic
updated 8.0 years ago by ▴ 300 • written 8.1 years ago by ▴ 50
0
votes
1
reply
1.9k
views
Error: could not find function "msaConvert"
msa software error
updated 8.2 years ago by ▴ 300 • written 8.2 years ago by • 0
0
votes
3
replies
1.8k
views
installation failed when trying msa
msa
updated 8.2 years ago by ▴ 300 • written 8.2 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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