- by /u/Spiritual-Feed-3296I rewrote Ensembl VEP in Rust. It's 130x faster. https://fastvep.org/ Got tired of waiting hours for VEP during my PhD, so I eventually just… rebuilt the whole thing (thanks to agentic coding). fastVEP annotates 4M+ WGS variants (full GIAB HG002, 508K transcripts) in about 1.5 minutes on my MacBook. Ensembl VEP can't finish that run on my notebook. On smaller subsets where both tools finish, fastVEP is 130x faster. Accuracy: 100% match across 23 fields on 2,340 transcript-allele pairs vs. VEP v115.1. I didn't cut corners — same GFF3, same FASTA, same flags. What's in it: – 49 SO terms, […]
- by /u/rikkibioinfoA 3-part hands-on RNA-seq tutorial series by Dr. Babajan Banaganapali (Bioinformatics With BB), covering the complete pipeline from raw reads to DESeq2 normalization and visualization. Part 1 — Introduction & Workflow (RNA-seq types, wet-lab steps, full pipeline overview) https://youtu.be/dq31baC_AHs Part 2 — QC, Alignment & Quantification (FastQC, Cutadapt, STAR/HISAT2, FeatureCounts — with real troubleshooting) https://youtu.be/4y2R2PgdBHo Part 3 — DESeq2 Normalization, Visualization & Interpretation (R, size-factor normalization, heatmaps, expression plots) https://www.youtube.com/watch?v=DxesV0eWtTQ Reproducible R and bash scripts are linked in each video description. submitted by /u/rikkibioinfo [link] [comments]
- by /u/PoseidonmagmaSomething that doesn't get talked about enough: 83.8% of global drug safety genomic research comes from European populations. When a drug gets approved, the safety evidence is almost entirely built on European genomes — then it's prescribed in India, Africa, East Asia, without adjustment. The consequences are real: Carbamazepine causes Stevens-Johnson Syndrome almost exclusively in carriers of HLA-B*15:02 — present in ~10% of Han Chinese, virtually absent in Europeans. European-majority Phase III trials never caught this. Clopidogrel fails as a prodrug in 57% of Pacific Islanders due to a metabolizer gene variant. Standard warfarin doses cause bleeding in East Asian […]
- by /u/Regular_TailorHey researchers or disgruntled lab managers! I'm a human trying to do an N of One study on a promising gene silencing hypothesis. We're trying to get 5-6 PAXgene tubes for collection. We don't have any institutional affiliation and we're 100% down to cover costs, but a pack of 100 is straining our household budget. Any help appreciated, DM with leads! submitted by /u/Regular_Tailor [link] [comments]
- by /u/bioinfoAgentYesterday, the new moderator flagged three of my replies as “breaks the be-kind rule” and overlooked other unfriendly replies to my post. This was all done because the MOD hates AI, and that was the main message of my post. Subjective decision destroy Reddit’s user experience. We must all ask Reddit to revoke this woke (meaning irrational, detached from reality) moderator and make [r/genomics](r/genomics) a place of unbiased scientific discourse. submitted by /u/bioinfoAgent [link] [comments]
- by /u/akenes96submitted by /u/akenes96 [link] [comments]
- by /u/Spiritual-Feed-3296Try it here: https://var-crawl.vercel.app/ https://github.com/Huang-lab/VarCrawl I don't think there's a need to publish this so want to promote here for people to use it, please help spread the word to whoever finds this helpful! submitted by /u/Spiritual-Feed-3296 [link] [comments]
- by /u/Holodoxasubmitted by /u/Holodoxa [link] [comments]
- by /u/Holodoxasubmitted by /u/Holodoxa [link] [comments]
- by /u/thewall888scAgent I’ve been working on an AI agent (scAgent) that can run end-to-end scRNA-seq analysis through natural language, and wanted to share it here for feedback from people who actually work with this data. The goal wasn’t just “chat with your data,” but something that can reliably execute real workflows — including handling partially processed datasets, tracking decisions, and staying reproducible. What it does in practice: Runs full pipelines: QC → normalization → HVG → PCA → batch correction → clustering → annotation (CellTypist) → DE (pseudobulk via DESeq2 / edgeR) → GSEA Accepts raw Cell Ranger output or .h5ad […]
- by /u/Holodoxasubmitted by /u/Holodoxa [link] [comments]
- by /u/bioinfoAgenthttps://preview.redd.it/ax9gsiqbn2vg1.png?width=3354&format=png&auto=webp&s=f14f4cc2afa326523a980388931f03d6e860710c I've been in bioinformatics for 20+ years and have been working on agentic pipelines for the past year. Ran into a problem that I think anyone using Claude Code or Codex for bioinformatics work has hit: The agent can write the code. It doesn't know the field. It'll chain tools together in an order that's plausible but not standard. Skip QC steps. Pick defaults that are technically valid but wrong for the data type. No provenance for any of it. Community-standard workflows live in papers and practitioner intuition, not in model weights. So I built Skill Graph. It's a […]
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