You keep telling me to submit an issue, so here you go.
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RNAvigate cannot handle expanded nucleotide alphabets (e.g. 'I' for inosine)
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Readthedocs has at least two versions floating around with vastly different information. Our collaborator found a deprecated version when I told them to use the readthedocs site and it created a lot of confusion. Bad link here (https://rnavigate.readthedocs.io/en/stable/loading-data/), good link here (https://rnavigate.readthedocs.io/en/latest/get_started/loading_data.html#). What I'm calling good link here is the version I use, so if there's another newer version, then some of these items may be obsolete.
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Readthedocs are difficult for new users to determine what are placeholder names/function calls/valid real names without concrete executable examples. A live notebook with a small example data set would help new user onboarding immensely.
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A readthedocs section on how to properly resize plots is needed (so domains, seqbar, etc. don't get totally messed up).
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I think varna structures still appear upside down by default (v1.0.0).
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There isn't a section on exporting/saving plots in the readthedocs. It may also be helpful to prominently point out the shortcut that users can drag and drop plots from a notebook directly to PowerPoint.
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RNAvigate is actually very good at parsing DBN and sequence info for a specific region of an RNA. These two functions are something I use often for generating airport terminal diagrams in other packages, and would likely be of wide interest to the community.
Sample-name-placeholder.get_data("ss").get_dotbracket()[100:150] #returns nt sequence for region 100-150 of Sample
Sample-name-placeholder.get_data("ss").sequence[100:150] #returns DBN for matching region 100-150 of Sample
- Plotting multiple related samples or deletion mutants on a shared x-axis space generated from a multi-sequence alignment was essential for the viral frameshifting paper and has come up a few times with other users. A readthedocs section on how to do this would be great.
You keep telling me to submit an issue, so here you go.
RNAvigate cannot handle expanded nucleotide alphabets (e.g. 'I' for inosine)
Readthedocs has at least two versions floating around with vastly different information. Our collaborator found a deprecated version when I told them to use the readthedocs site and it created a lot of confusion. Bad link here (https://rnavigate.readthedocs.io/en/stable/loading-data/), good link here (https://rnavigate.readthedocs.io/en/latest/get_started/loading_data.html#). What I'm calling good link here is the version I use, so if there's another newer version, then some of these items may be obsolete.
Readthedocs are difficult for new users to determine what are placeholder names/function calls/valid real names without concrete executable examples. A live notebook with a small example data set would help new user onboarding immensely.
A readthedocs section on how to properly resize plots is needed (so domains, seqbar, etc. don't get totally messed up).
I think varna structures still appear upside down by default (v1.0.0).
There isn't a section on exporting/saving plots in the readthedocs. It may also be helpful to prominently point out the shortcut that users can drag and drop plots from a notebook directly to PowerPoint.
RNAvigate is actually very good at parsing DBN and sequence info for a specific region of an RNA. These two functions are something I use often for generating airport terminal diagrams in other packages, and would likely be of wide interest to the community.
Sample-name-placeholder.get_data("ss").get_dotbracket()[100:150] #returns nt sequence for region 100-150 of Sample
Sample-name-placeholder.get_data("ss").sequence[100:150] #returns DBN for matching region 100-150 of Sample