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All Tools at a Glance

Quick reference table of all available tools organized by category.

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Data Conversion & Processing (12 tools)

ToolDescriptionPrimary Use
first_k_lines_of_csvPreview first K lines of CSVData preview and structure understanding
csv_to_vcfConvert CSV to VCF formatFormat conversion for genomic analysis
convert_xlsx_to_csvTransform Excel to CSVFormat conversion between delimited files
convert_tsv_to_csvConvert TSV to CSVFormat conversion between delimited files
create_csv_from_dataGenerate CSV from structured dataCreate datasets from query results
genomic_to_vcfConvert genomic formats to VCFStandardize genomic file formats
check_vcf_compatibilityValidate VCF file complianceFile validation and format checking
convert_ids_in_csv_using_vcfMap identifiers using VCFIdentifier mapping and conversion
index_vcfCreate VCF index filesOptimize VCF file access and querying
filter_vcf_by_rsidsFilter variants by RSIDsExtract relevant variants from VCF
filter_vcf_by_genesExtract variants from genesGene-based variant filtering

View Detailed Documentation

Complete guide with examples and workflows

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Analysis & Querying (8 tools)

ToolDescriptionPrimary Use
analyze_csvStatistical analysis on CSVStatistical analysis and data exploration
run_sql_queryExecute SQL on genomic dataDirect database query execution
build_sql_query_for_csvGenerate SQL from CSV structureAutomated query generation
run_sql_query_from_fileExecute stored SQL queriesFile-based query execution
describe_csv_columns_with_htmlGenerate column documentationColumn documentation generation
describe_csv_columns_with_html_smartIntelligent column analysisAdvanced column analysis and insights
make_example_tableCreate sample tablesGenerate sample data tables
get_gene_networkRetrieve gene interactionsGene relationship discovery

View Detailed Documentation

Complete guide with examples and workflows

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ANOVA Tools (12 tools)

ToolDescriptionPrimary Use
anova_analysisPerform ANOVA testsStatistical variance analysis
plan_anova_inputsValidate ANOVA inputsInput preparation and validation
anova_with_vcfANOVA on VCF dataVariant-based ANOVA analysis
anova_sql_queryBuild SQL for ANOVADatabase-backed ANOVA operations
anova_id_conversionConvert identifiersIdentifier mapping for analysis
anova_wes_id_mappingMap WES sample IDsWES data sample mapping
anova_rsids_for_genesExtract RSIDs for genesGene-to-variant mapping
anova_filter_by_rsidFilter by RSIDVariant-specific result filtering
anova_filter_coding_variantsFilter coding variantsCoding sequence variant selection
anova_cohort_allele_freqCalculate cohort frequenciesPopulation frequency calculations
anova_reference_allele_freqGet reference frequenciesBenchmark frequency data
anova_freq_diff_topkTop K by frequency diffVariant prioritization by frequency

View Detailed Documentation

Complete guide with examples and workflows

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GWAS Tools (4 tools)

ToolDescriptionPrimary Use
plan_plink_gwas_inputsPlan PLINK inputsGWAS workflow preparation
run_plink_gwasExecute GWAS analysisRun GWAS analysis
create_manhattan_plotGenerate Manhattan plotsGWAS results visualization
generate_gwas_sample_dataCreate sample datasetsTest data generation

View Detailed Documentation

Complete guide with examples and workflows

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Knowledge Base (1 tool)

ToolDescriptionPrimary Use
search_knowledge_baseRAG-powered searchSemantic search and information retrieval

View Detailed Documentation

Complete guide with examples and workflows

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Common Workflows

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Basic Data Processing

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GWAS Analysis Pipeline

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Complete ANOVA Workflow

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Part C: Input Prep & ANOVA

  1. sql_query – Filter phenotype data with SQL
  2. id_conversion – Convert subject IDs and prepare phenotype table
  3. wes_id_mapping – Map phenotype IDs to WES column names
  4. rsids_for_genes – Extract rsIDs for gene lists
  5. filter_by_rsid – Filter variants by RSID list
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Part D: Filtering & Frequency Analysis

  1. filter_coding_variants – Filter variants to coding rsIDs only
  2. cohort_allele_freq – Compute cohort allele frequencies
  3. reference_allele_freq – Look up European reference frequencies
  4. freq_diff_topk – Select top frequency differences (two-sided)
  5. anova – Run ANOVA analysis per RSID (final step)

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Tool Selection Guide

Start with Data Conversion & Processing tools:
  • Excel to CSV: convert_xlsx_to_csv
  • TSV to CSV: convert_tsv_to_csv
  • CSV to VCF: csv_to_vcf
  • Any genomic format to VCF: genomic_to_vcf
Use Analysis & Querying or ANOVA tools:
  • General statistics: analyze_csv
  • Group comparisons: anova_analysis
  • Variant associations: anova_with_vcf
  • Custom queries: run_sql_query
Use GWAS Tools in sequence:
  1. plan_plink_gwas_inputs - Validate inputs
  2. run_plink_gwas - Run analysis
  3. create_manhattan_plot - Visualize results
Multiple filtering options available:
  • By RSIDs: filter_vcf_by_rsids or anova_filter_by_rsid
  • By genes: filter_vcf_by_genes
  • Coding variants only: anova_filter_coding_variants
Use the Knowledge Base:
  • search_knowledge_base - Natural language search for any genomic concept

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Filter Tools by Feature

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Supports VCF Files

  • csv_to_vcf
  • genomic_to_vcf
  • check_vcf_compatibility
  • index_vcf
  • filter_vcf_by_rsids
  • filter_vcf_by_genes
  • convert_ids_in_csv_using_vcf
  • anova_with_vcf

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Statistical Analysis

  • analyze_csv
  • anova_analysis
  • plan_anova_inputs
  • anova_with_vcf
  • run_plink_gwas

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Frequency Calculations

  • anova_cohort_allele_freq
  • anova_reference_allele_freq
  • anova_freq_diff_topk

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Visualization

  • create_manhattan_plot
  • describe_csv_columns_with_html
  • describe_csv_columns_with_html_smart

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SQL/Database

  • run_sql_query
  • build_sql_query_for_csv
  • run_sql_query_from_file
  • anova_sql_query

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Need Help Choosing?

Tools Overview

High-level overview and common workflows

Search Knowledge Base

Ask questions about which tool to use

Data Conversion

File format conversion and processing

Analysis Tools

Statistical analysis and querying