B. Arman Aksoy
B. Arman Aksoy
All right — continuing my scattered idea storms: one of the things I realized running all those pipelines over and over again (to workaround random middle-node failures) was that we...
Instead of relying on the detection logic, we can explicitly pass the reference genome to the topiary within biokepi.
Following up on @julia326 talk, might worth looking into these tools and see whether we can get them into biokepi: - Variant annotation 1. [snpEff](http://snpeff.sourceforge.net/SnpEff.html) 2. or extend [varcode](https://github.com/hammerlab/varcode) to...
As @rleonid pointed out, `bioconda` channel seems to have quite a bit of recipes covering many of the bases in the Bioinformatics field. Since `bioconda` is, by default, a supported...
...ver the back element. Changed the parameter `content` to the HTML element--that is the back of the card/modal--with the name `back`. The older way was flawed in the sense that,...
Currently have 36309e2210e4e2a4473e74fb8acc071a5fb6d5da cloned and downloaded the `PubMedQA` on 2/3/2023: ```bash $ md5sum checkpoints/QA-PubMedQA-BioGPT.tgz 8d05745c9cd93ce3a7b4d87251823b67 checkpoints/QA-PubMedQA-BioGPT.tgz ``` Following the advice under #23, I was able to make some progress but...
Hi there, This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's `-max_target_seqs` parameter: - [scripts/annotation/blast_script.sh](https://github.com/jimmyodonnell/banzai/blob/18a97e983543ffb17e2bf57896ad12ec755adb37/scripts/annotation/blast_script.sh)...
Users currently need to download files manually one by one and then switch to one of the analysis tabs to run a particular analysis of interest. Assuming that the GUI...
**work in progress** This will help support `pdflatex` users. The conversion is done via `convert` tool, so we now mention this optional dependency in README file.
This is in conjunction with issue #4 and also related to issue #6. It is a really good idea to fetch the names automatically from GitHub (see issue #4), but...