User: Erik Wright

gravatar for Erik Wright
Erik Wright140
Reputation:
140
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Website:
http://DECIPHER.codes/
Twitter:
digitalwright
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
2 years ago
Email:
d************@gmail.com

Posts by Erik Wright

<prev • 18 results • page 1 of 2 • next >
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Comment: C: PCR simulation with PNAs
... Thanks for your question. `AmplifyDNA()` is intended solely for DNA oligonucleotides. PNAs require different thermodynamic parameters that are not supported by `AmplifyDNA()`. You may want to look for alternative solutions in [this reference][1]. [1]: https://www.tandfonline.com/doi/abs/10.3109/0 ...
written 6 weeks ago by Erik Wright140
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Answer: A: Display BrowseSeqs output in R Notebook?
... We have figured out a workaround for displaying external html code inside R Notebooks. It is not exactly the same as displaying it in a browser window by itself, but it is better than nothing. First you tell `BrowseSeqs()` to write the html output to a specific file, and then you use `htmltools::inc ...
written 9 weeks ago by Erik Wright140
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Comment: C: Updating release branch from devel
... It looks like that worked!  Thanks for your help. ...
written 18 months ago by Erik Wright140
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Updating release branch from devel
... The latest version of RSQLite (on CRAN) broke my package, DECIPHER, in both the devel and release branches.  I have patched the devel branch so that it should work in the next build, but I do not understand the instructions on how to merge the changes into the release branch.  Does anyone have the m ...
git written 18 months ago by Erik Wright140 • updated 18 months ago by Martin Morgan ♦♦ 24k
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Comment: C: How to get sequence homology percent from a multiple sequence alignment in DECIP
... The outputs of DistanceMatrix, including examples, are described in: ?DistanceMatrix Generally, it is a matrix containing the distance between each pair of input sequences.  The distance is 1 - the similarity (fraction of sites that are identical). Homology is not well defined in this context, b ...
written 18 months ago by Erik Wright140
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Comment: C: How to get sequence homology percent from a multiple sequence alignment in DECIP
... Just to clarify, do you mean that you would like to get a distance matrix? d <- DistanceMatrix(bod_aa) And then look at the distances to a specific sequence (e.g., #1)? d[1,] ...
written 18 months ago by Erik Wright140
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Comment: C: Transform index to chromosome in DECIPHER package
... Thanks for clarifying your question.  The sequences are numbered (indexed) according to their order in the imported file.  You can query the sequence headers from the database, for example with: desc <- dbGetQuery(dbConn, 'select description from Seqs where identifier is "Genome2"') desc$descri ...
written 22 months ago by Erik Wright140
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Answer: A: Transform index to chromosome in DECIPHER package
... Thanks for your interest in DECIPHER. The synteny object that is output by FindSynteny is defined in Synteny-class, see: ?`Synteny-class` Since you have 3 genomes, your Synteny object will be a 3 x 3 matrix, each each cell containing a list.  Therefore, synteny[[6]] corresponds to the lower tria ...
written 22 months ago by Erik Wright140
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Comment: C: Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
... Of course, simply add a conditional above the AlignSeqs() call: if (length(combAA) > 1) aligned_list[[i]] <- AlignSeqs(combAA) ...
written 22 months ago by Erik Wright140
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Comment: C: Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
... This error means that you are trying to combine disparate classes.  Probably because the variable seq needs to be converted to an AAStringSet: seq <- AAStringSet(seq) ...
written 22 months ago by Erik Wright140

Latest awards to Erik Wright

Scholar 2.0 years ago, created an answer that has been accepted. For A: Is it possible to import a multiple fasta alignemnt (.mfa) file into DECIPHER?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Colour a phylogenetic tree, based on column in DECIPHER?
Scholar 2.0 years ago, created an answer that has been accepted. For A: Is it possible to do an alignment to a chosen reference sequence in DECIPHER?

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