Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR.
Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments.
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples.
Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions.
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discove — from…
Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011),…
Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes.
Cross-method decision tree for calling hits in pooled CRISPR screens. Catalogs statistical models (MAGeCK RRA, MAGeCK MLE, BAGEL2, drugZ, JACKS, Chronos, CERES), experimental…
Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif, and statannotations with correct test selection (parametric…
Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters — from…
Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent…
Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods.
Defines cell populations in flow and spectral cytometry through manual gates (rectangle, polygon, quadrant, boolean) and reproducible automated gating (openCyto gating templates,…
Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data.
Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data.
Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize diffe — from…
Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize diffe — from…
Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing.
Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing.
Evaluates scientific research rigor using systematic frameworks. Assesses methodology, statistics, biases, and evidence quality.
Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods.
Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods.
Statistical analysis for metabolomics data. Covers univariate testing, multivariate methods (PCA, PLS-DA), and biomarker discovery.
Per-CpG differential methylation testing from bisulfite sequencing count data or beta-value matrices.
DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons.
DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons.
Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression — from…
Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression — from…
Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLI — from…
Python population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using Genot — from…
Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics.
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython.
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython.
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck.
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck.
End-to-end post-GWAS causal inference pipeline orchestrating heritability partitioning, genetic correlation, Mendelian randomization with CHP-aware sensitivity (CAUSE / LHC-MR),…
End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statis — from…
End-to-end metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, normalization, statistical analysis, and pathway mappi — from…
Query Danish real estate data from Boliga.dk as pandas DataFrames. Use when the user asks about Danish property prices, real estate searches, market statistics, or housing…
Display comprehensive project progress including BRD status, corpus statistics, research progress, and writing progress with recommendations for next actions
Display LOCAL BTR statistics (NOT ByteRover/brv). Use when the user asks "how much time saved", "context statistics", "usage metrics", "BTR statistics", "BTR metrics", "BTR…
Constructs stat arb strategies with pair selection, signal generation, and portfolio optimization under market neutrality constraints.
Pull a Lee-branded BAO-style Business Key Facts PDF (3-page landscape) for any NC address. Returns key statistics, households table, site map with 1/3/5 mile rings, education…
Analyzes the codex cache and generates comprehensive statistics about cache performance, storage usage, and health status. Delegates to fractary CLI for cache analysis operations.
Interactive sample size calculator for medical research. Decision-tree guided test selection, reproducible R/Python code, effect size interpretation, and IRB-ready justification…
Search and query Calibre library databases. Use when the user asks about books, TBR (to-be-read), reading lists, Calibre library queries, book searches, or mentions Calibre.
Searches LinkedIn Jobs, Glassdoor, and Levels.fyi for open roles matching your configured target criteria.
Use when building or auditing multi-panel mechanistic figures and tables for a Cancer Cell (Cell Press) manuscript — quantification of images, panel logic, image integrity, and…
Comprehensive toolkit for detecting and eliminating "AI slop" - generic, low-quality AI-generated patterns in natural language, code, and design.
Automatically discover API design skills when working with REST APIs, GraphQL schemas, API authentication, OAuth, JWT, rate limiting, API versioning, error handling, or e — from…
Automatically discover build system skills when working with build systems. Activates for build-systems development tasks. — from science/math-stats
Automatically discover caching and performance skills when working with caching. Activates for caching development tasks. — from science/math-stats
Automatically discover CI/CD and automation skills when working with CI/CD. Activates for cicd development tasks. — from science/math-stats
Automatically discover cloud computing and serverless skills when working with cloud. Activates for cloud development tasks. — from science/math-stats
Automatically discover collaboration and teamwork skills when working with collaboration. Activates for collaboration development tasks. — from science/math-stats
Automatically discover container and Docker skills when working with Docker. Activates for containers development tasks. — from science/math-stats
Automatically discover data pipeline and ETL skills when working with ETL. Activates for data development tasks. — from science/math-stats
Automatically discover database skills when working with SQL, PostgreSQL, MongoDB, Redis, database schema design, query optimization, migrations, connection pooling, ORMs — from…
Automatically discover debugging and profiling skills when working with debugging. Activates for debugging development tasks. — from science/math-stats
Automatically discover deployment and release skills when working with deployment. Activates for deployment development tasks. — from science/math-stats