u/MarioFld

Non-technical people like to use the WGSextract tool for this purpose - https://wgsextract.github.io/ .

Since no such thing seems to exist: wouldn't this be a nice addition to the `devout` package? Like a `sixel()` device similar to the already existing`ascii()` device?

Thank you kindly for the help!! Ouch, for not thoroughly checking the manual.

I also dived a bit more into the health reports and found some issues that could not convincingly be explained by Nebula Genomics (analysis here). I was therefore interested in other ways to compute polygenetic scores using open-source tools. I was curious how the results would differ. While I still think there are some bugs in the calculation from Nebula Genomics, I think their general approach of calculating the PRS is easier to understand and follow than some other alternatives, which is a benefit for the user group.

I am interested in the same issue as the OP:

I'd like it to be possible to copy text+images to other applications.

Basically, I would like to copy a selection of a document including both text and images and paste it to an external application, for example at GitHub.

Could you give more details? I have the plugin activated, and copy and paste does still not include images for me.

I found the "Copy document as HTML" plugin which allows you to copy a selection with images to Word. But if you would like to copy the GFM markdown with images to GitHub, the HTML is not of help.

Edit: Ah, I see that you can copy the image itself. But not a selection with both text and images. Any idea if this is possible?

Thank you! Good point to mention the trait reports. So far, I did not plan to write an article because there are only a few of them, they are very short and there is not much room for discussion. One can quickly double-check the own genotypes with information on SNPedia on the 1-3 DNA variants mentioned in the trait reports. So I expected a potential article to be too boring. Anything specific you would be interested in?

For me too. Took about 8 weeks, but the DNA sample quality was still fine!

I did not compare them, but I did an analysis of Nebula Genomics reports here. I think the reports have a different scope: Promethase focuses on single SNPs whereas Nebula Health reports focus on polygenetic risk scores.

If you are interested in the raw sequencing/variant data, and have a geneticist at hand to help with interpretation, it might be an option. The raw data is quite good, see my article at https://mfasold.net/blog/assessing-nebula-genomics-dtc-wgs/

I have the error when I type a single quote after two double quotes. It would be super helpful if you had a pointer to the known bug in Emacs 28.

Thank you. A package like yours is helpful for conveniently getting the chatgpt responses into Emacs. But I would like to go one step further. If I have the prompt "Proofread this text: [Text]", I want the chatGPT response to be compared with the original [Text], so that I can then accept/decline the suggested changes individually. Like the suggest-mode in Word/Google Docs, but within Emacs.

The future will start running immediately when spawn is called (see https://docs.rs/tokio/1.28.1/tokio/runtime/struct.Runtime.html#method.spawn )

Hisat2 is probably the classical alternative. However, last I checked, it did not completely implement the detection/exporting features for novel splice junctions. So if you work on splice junction detection, you might need to fall back to TopHat2, the predecessor of Hisat2.

Good question. I cannot answer why exactly cnvkit uses the R package DNAcopy instead of this python implementation. However, the cbseq package unfortunately has a restrictive GPL2 license.

It is worth noting that flycheck (and therefore this package) does not provide a way to apply corrections.

I have a proposition that is both an interesting algorithm and also would be a valuable addition to the community: An Implementation of circular binary segmentation (CBS) that integrates with cnvkit. Cnvkit is widely used for the detection of copy numbers, and the best (and default) method for segmentation is CBS based on the R package PSCBS. However, it's a huge overhead to install R and many dependencies to run PSCBS. Also, a new implementation could be more performant and have a more permissive license. I think this would be much appreciated.

I would say maybe 1/4 goes for a PhD and it makes sense for academia and pharma. For biotech/labs/other industry it is often not required.

.cel files are created from Affymetrix microarraysl experiments. So I don't think you have Chip-Seq data. The best way to analyze is using R/bioc packages.