Analyze SDRF files to detect experimental design flaws and generate MSstats contrast suggestions.
npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-design
Please help me install this Agent Skill. Skill: sdrf:design Source: https://github.com/bigbio/sdrf-skills/tree/main/skills/sdrf-design Command: npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-design
The skill helps users assess the experimental design captured in an SDRF file, identifying batch effects, confounding variables, and replication issues that can compromise downstream analysis.
Ask the skill to analyze your SDRF file and provide a design report.
High-intent search queries and answers about installing and using this skill.
To detect batch effects and confounders in an SDRF file, cross-tabulate factor values against technical variables like instruments and TMT labels. This analysis flags perfect or partial confounds, evaluating condition balance before statistical analysis.
Generating MSstats contrast matrices from an SDRF design involves extracting conditions and replicates to produce comparison guidance. The analysis suggests appropriate contrasts based on the evaluated biological groupings captured in the SDRF.
SDRF experimental design analysis evaluates proteomics datasets for condition balance, instrument usage, and sample grouping. You need it before statistical analysis to identify inadequate replication and technical confounders that compromise downstream results.
You can assess biological replication adequacy using an SDRF file by evaluating biological and technical replicate counts within the experimental design. This replication assessment evaluates sample grouping and suggests statistical power for the study.
Analyzing SDRF files for design flaws requires no external dependencies. The analysis processes the SDRF content directly to generate a structured summary, confounder flags, and contrast suggestions without needing additional software libraries.
bigbioValidate SDRF files for structural, template, and ontology issues.
inflexa-aiPerform differential expression analysis on quantitative proteomics data using limma and MSstats.
mims-harvardRetrieve gene expression and multi-omics datasets from ArrayExpress and BioStudies.
bigbioAnswer SDRF specification questions using official spec data files.
