21 skills found
brycewang-stanford / review-papRun a 6-agent pre-submission review of a pre-analysis plan (PAP) for a specified registration target or journal
FreedomIntelligence / bio-bedgraph-handlingbedGraph is a text format for displaying continuous-valued data on genome browsers. Common for coverage, signal intensity, and scores.
FreedomIntelligence / bio-data-visualization-specialized-omics-plotsThis skill provides reusable plotting functions for common omics visualizations that can be applied across different analysis types: - Volcano plots (any DE result) - MA plots (any log-fold-change data) - PCA plots (any high-dimensional data) - Enrichment dotplots (manual, not enrichplot) - ExpressiâĻ
FreedomIntelligence / bio-alignment-indexingCreate indices for random access to alignment files using samtools and pysam.
FreedomIntelligence / bio-alignment-sortingSort alignment files by coordinate or read name using samtools and pysam.
FreedomIntelligence / bio-alignment-validationPost-alignment quality control to verify alignment quality and identify issues.
FreedomIntelligence / bio-codon-usageAnalyze codon usage patterns and calculate codon adaptation metrics using Biopython.
FreedomIntelligence / bio-data-visualization-circos-plotsCircular genome visualizations for displaying multiple data tracks around chromosome ideograms.
FreedomIntelligence / bio-genome-assembly-assembly-qcEvaluate genome assembly quality with contiguity metrics (QUAST) and gene completeness (BUSCO).
FreedomIntelligence / bio-genome-intervals-bed-file-basicsBED (Browser Extensible Data) format stores genomic intervals. Uses 0-based, half-open coordinates.
FreedomIntelligence / bio-genome-intervals-bigwig-tracksBigWig is an indexed binary format for continuous genomic data. Efficient for genome browsers and programmatic access.
FreedomIntelligence / bio-genome-intervals-coverage-analysisCalculate coverage and depth across genomic regions using bedtools and pybedtools.
FreedomIntelligence / bio-genome-intervals-gtf-gff-handlingGTF and GFF3 are standard gene annotation formats. Both use 1-based coordinates.
FreedomIntelligence / bio-genome-intervals-interval-arithmeticCore set operations on genomic intervals using bedtools (CLI) and pybedtools (Python).
FreedomIntelligence / bio-genome-intervals-proximity-operationsOperations for finding nearby features and extending intervals using bedtools and pybedtools.
FreedomIntelligence / bio-geo-dataQuery and access Gene Expression Omnibus datasets using Biopython's Entrez module.
FreedomIntelligence / armored-cart-design-agentThe Armored CAR-T Design Agent provides AI-assisted design of next-generation armored CAR-T cells engineered to express cytokines, chemokines, or other enhancing factors.
FreedomIntelligence / bio-experimental-design-power-analysisPower = probability of detecting a true effect. Underpowered studies waste resources; overpowered studies are inefficient.
FreedomIntelligence / bio-experimental-design-multiple-testingTesting 20,000 genes at p < 0.05 yields ~1,000 false positives by chance. Correction is essential.
FreedomIntelligence / bio-alignment-files-bam-statisticsGenerate alignment statistics using samtools and pysam.
FreedomIntelligence / bio-experimental-design-batch-designBatch effects are unavoidable. Good design makes them correctable.
