I would like to see better pure bioinformatics centromere predictors too. I only know of Centrominer which does not work well for me on various plant genomes. https: github.com aaranyue quarTeT Other than that I try to do repeat finding using EDTA, TRF, Red etc and piece it all together manually....

   Thank you very much for the feedback. I’ve now added a new gallery directory to the BIOSZEN GitHub repository with app screenshots and example outputs for each plot type (boxplot, barplot, violin, curves, stacked, correlation, etc.) so it’s easier to quickly see what the tool does before installing...

   Show some screenshots of your tool in the docs. Sell it to us. Convince us with some pretty plots that your tool is worth running. Few people have the time to go install a tool that they don’t know what it does.

   One suggestion for your READMEe is to provide a realistic example. Say take the representative viral genome from NCBI, those reasonably small and demonstrate the tool via those examples. Right now your examples are input.fasta and output.csv and the reader has no idea what is inside these files,...

   Bumping threads solely for visibility is not acceptable on Biostar. This is against Biostar etiquette and makes it harder for others to get fair visibility. Posts should only be updated when there is new information or a substantive follow-up that adds important information not originally available...

   I’m sharing BIOSZEN , a lightweight R Shiny application for data analysis and visualization based on Excel input files. It is designed for quick exploratory analysis and publication-ready plots without needing to write code. What BIOSZEN does Generates common plots from Excel tables: boxplots, bar...

   Hi, I’m happy to share Blini , a new tool for sequence lookup and dereplication at massive scales, where traditional tools like BLAST or locally-run software might hit resource limits. What is Blini? Blini is an algorithm for quick nucleotide sequence lookup and dereplication. It combines several k...

   You could do something like the following to extract fungal sequence entries from nr preformatted database (you will need to download the files for it) using a program provided in the blast package. blastdbcmd -db nr -taxids 4751 -outfmt %a -out fungal.fa then use makeblastdb to create your custom...

   I am trying to do exactly this. I would like to make a custom database with proteins from Fungi, my taxids would be 4751. Would you mind sharing your code ?

   You would need to run CellChat on every WT-KO individual mice pair to find that. I wonder whether it is meaningful to do that since usually you would want significant results that hold true in your group comparison, not in individual mice but not the group. What I would do (and have done before) is...

   From miRNAtissue atlas: https: web.ccb.uni-saarland.de mirnatissueatlas 2025 patterns hsa Atlas 2025 tissue rpmm mirna hsa-miR-383-5p yes organ no

   Hey people, I asked this question on a few other forums too, but I think my chances of getting an answer on any of single forum are modest, so I want to ask here too, if that’s okay. Anyway, to the point: using CellChat (v2.2.0), when comparing between two groups (WT vs. KO,), each of which...

   I’m implementing CNV SV annotation and seeing a common issue: OMIM gene to phenotype mappings explode for multi-gene events and swamp the output. Right now we map overlapped genes to OMIM phenotypes and score them against case HPO terms, but we still get long, low-specificity lists. Inputs: CNV SV...

   Let me show you how to properly format a post.

   Hello I have a question regarding miRNA expression data. For example, I have information that hsa-miR-383-5p is downregulated in Ovarian Cancer cells. I want to know what is the status of this particular miRNA across all other tissues (whatever is available in the database). Eagerly waiting for...

   If you are conducting bioinformatics research, especially when dealing with GEO (Gene Expression Omnibus) data, you may have used the [GEOmetadb](https: github.com zhujack GEOmetadb) package. While it was once a great tool, unfortunately, it has not been updated for years. Additionally, the...

   I have never worked with Geneious Prime so what I am about to say might be my bias talking rather than an informed opinion. Commercial programs of that type are rarely best tools for anything other than being most convenient for the users who want to use a point-and-click interface. So count...

   www.p3scorp.com

   Hi all In your opinion, which is the best tool to anotate ORFs in viral metagenomics? I have some tick samples I want to do the viral characterization of, however I was told to annotate the ORFs with Geneious Prime, but I can t afford it so, which is the next best option?

   I have solved it It was a corrupt installation of BSgenome. Here is the GitHub that helped me: https: github.com Bioconductor BSgenomeForge pull 46 [enter link description here][1] [1]: https: github.com Bioconductor BSgenomeForge pull 46

   Hey everyone I followed this tutorial ([https: support.bioconductor.org p 125514 ][1]) in order to create a package for Papio anubis genome from NCBI. I originally wanted to use Ensembl’s assembly but BSgenome mainly takes UCSC and NCBI. Here is my seed file: Package: BSgenome.Panubis.NCBI.Panubis1...

   W::bgzf read block] EOF marker is absent. The input may be truncated check the .g.vcf.gz files under home user epi2melabs instances wf-trio 01KEQ7QEFVGWP2B7SDZY9QCBQR work b8 66ca4c29765eee361abf0c4e9fa3f5 are not truncated. something like: find home user epi2melabs instances wf-trio...

   Hi all, My sincere apologies for the issues you are experiencing with Ensembl. We are aware of the site’s performance problems, which unfortunately have become more common as the codebase ages, datasets grow and our resources shift increasingly towards developing the new Ensembl site beta.ensembl...

   https: p3scorp.com jobs bioinformatician-scientist This link (or a similar one) may have been included in the original posting. It does not seem to be there now.

   Strange. This site considers it down for everyone. https: www.isitdownrightnow.com ensembl.org.html But it does work using Chrome for me too.