Query Snaptron for splice junction counts, RNA-seq metadata, and BigWig coverage.
npx skills add https://github.com/bfairkun/dotfiles --skill snaptron-bfairkun
Please help me install this Agent Skill. Skill: snaptron Source: https://github.com/bfairkun/dotfiles/tree/main/agents/.agents/skills/snaptron Command: npx skills add https://github.com/bfairkun/dotfiles --skill snaptron-bfairkun
High-intent search queries and answers about installing and using this skill.
Use the snaptron endpoint with a gene or region, e.g. GET https://snaptron.cs.jhu.edu/srav2/snaptron?regions=GAPDH, optionally filtered by sample rail_ids via sids. Results return as TSV with per-sample counts in the samples column.
Use the samples endpoint with sfilter, e.g. sfilter=cell_line:HeLa on srav2. Note srav3h has no cell_line field; search study_title, study_abstract, or sample_description instead.
srav2 covers ~49K recount2 human samples with cell_line and run_acc fields, while srav3h covers ~316K recount3 samples but uses sample_acc and lacks cell_line. srav3h data freezes around March 2021 and has no bigwig_file field.
For srav2, combine study_accession and run_accession: https://duffel.rail.bio/recount/{study}/bw/{run}.bw. For srav3h, use the recount3 base_sums path pattern with study and run suffix subdirectories.
The MCP client's fetch_samples creates a broken pandas MultiIndex for srav3h ids= queries. Parse the TSV response directly with csv.reader instead, as shown in the manual metadata fetching example.
Yes, IGV streams BigWigs directly from duffel.rail.bio URLs using HTTP range requests. Generate a session XML with Resource and Track elements pointing to the remote BigWig URLs and open it via File > Open Session.
Org-GAgentQuery gene, sequence, and variant data from the Ensembl REST API.
stellaromicsOrchestrate RNA-seq alternative splicing workflows from STAR alignment to rMATS-turbo results.
stellaromicsGenerate clustered heatmaps from gene expression or omics matrices with annotations.
omicverseProduce aligned BAM files and gene count matrices from SRA or FASTQ inputs.
