Biostrings
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Bioconductor
Efficient manipulation of biological strings
How do I use BString / BStringSet for values > 127? PacBio data uses 0:255 ranges for fp/rp/fi/ri tags. I am trying to use BioStrings to work with these tags....
In the following examples I'd expect `trimLRPatterns` to always leave `ATCG`: ``` r library(Biostrings) subject DNAStringSet object of length 1: #> width seq #> [1] 4 ATCG trimLRPatterns(subject = subject,...
```r library(Biostrings) example(readQualityScaledDNAStringSet, echo=FALSE) ## Warning messages: ## 1: In XStringSet("DNA", x, start = start, end = end, width = width, : ## metadata columns on input DNAStringSet object were...
Currently, `consensusString` fails for length-0 inputs: ``` r Biostrings::consensusString(character(0)) #> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'consensusString': 'x' has no...
@jwokaty Take a look at the changes [PDF](https://bioconductor.org/packages/release/bioc/vignettes/Biostrings/inst/doc/MultipleAlignments.pdf) and [HTML](https://rpubs.com/BerylK/982733) for comparison Issues I have: 1. - In the description file when writing authors using this format ``` Authors@R: c(...
Adds extended argument support to `matchProbePair` as requested in #29. New version implements `...` to match any argument in `matchPattern`, including the `fixed` argument for ambiguity code. Documentation updated accordingly.
Hi Hervé, @hpages Is there a function that takes a string, e.g., `MetThrGly` and converts to "MTG"? If not and within scope, I can work on implementing one using `AMINO_ACID_CODE`....
hi there, I've been reading in some multiple sequence alignments, as DNAStringSet objects. They're nucleotide alignments that encode proteins. I've been playing with using 'translate', but it looks like it's...
I am getting the following error when trying to convert a string to a DNAString: Error in as(mcols, mcols_target_class) : no method or default for coercing “DFrame” to “DataTable_OR_NULL” I...
