Madeline Page

Hello, I am new to proteomics and am trying to understand the mzTab output file. Specifically, I am looking for information about the `opt_` columns and how to interpret the...

New feature to allow ggsave to save multiple plots to separate pages of pdf

3

It would be super great if `ggsave()` could save multiple plots to the same pdf (on different pages). I think ideally, the plot argument would be able to be passed...

The isoform_id in isoformFeatures and exons does not match

2

@kvittingseerup We are trying to run this tool with output from Bambu but we are getting this error: ``` Error in createSwitchAnalyzeRlist(isoformFeatures = myIsoAnot, exons = myExons, : The isoform_id...

pretraining the nucleotide-transformer

3

Hi, I would like to pre-train the model myself to gain a better understanding of machine learning models. Specifically, **could you provide the code that was used to pre-train the...

### Description I ran into an issue, where I had a huge matrix with a lot of zeros in it. When those 0's were loaded in, they were converted to...

I would really appreciate a parameter for writing to files that would strip off unnecessary characters to save space. For example: 0.0 --> 0 5.0 --> 5 0.034 --> .034...

Add an option to output the transcript/gene counts for all the available options for a single run

1

Hi, I'm working on using IsoQuant, and it would be really useful for my workflow if I was able to get the output count matrices for multiple `--transcript_quantification` methods. For...

Hi! In the SegmentNT paper, there is this section in the methods. I'm wanting to calculate the MCC value for the predictions I received using SegmentNT. Would you be able...

Add the ability to 'split'/'collate' the groupTuple results

1

## New feature It would be really nice to have a way to 'collate' files in a groupTuple, so that I can have multiple groups of files for the same...

Use CPAT for the ORF

2

I'm using CPAT3. I know that the `analyzeNovelIsoformORF()` will determine ORF for my novel isoforms, but could the tool be modified to use the ones I get from CPAT? CPAT3...