FreedomIntelligence
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- ▌ Profile Report 2 · freedomintelligence bundleUnified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.
- ▌ Profile Report · freedomintelligence bundleUnified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.
- ▌ Blender Pipeline · freedomintelligence bundleExtract a tutorial or reconstruct a Blender result from video links, local videos with supporting assets, or Markdown tutorials in Codex chat. Clarify the intended output when unspecified; also route explicit showcase reproduction and independent asset edits.
- ▌ Blender Existing Asset Editing · freedomintelligence bundleEdit a declared part of an existing Blender project while preserving its authored composition, verifying non-target stability, and producing a reopen-verified receipt. Use for material, color, geometry, modeling, or scene edits; use a generation workflow when the whole asset must be created from zero.
- ▌ Blender Pipeline Generation · freedomintelligence bundleGenerate an editable Blender asset or animation from a blank scene, either by replaying verified tutorial-video evidence or by executing a model-direct generation task. Use for from-zero reconstruction; use the edit pipeline when an existing scene or asset must be modified.
- ▌ Blender Pipeline Reproduction · freedomintelligence bundleReproduce a maintained Blender showcase recipe from authorized video, tutorial, image, or local asset inputs while enforcing visual-acceptance and asset-distribution gates.
- ▌ Video To Visual Tutorial · freedomintelligence bundleTurn software or creative-workflow videos into evidence-grounded tutorials. Default visual mode uses local images and a 100-point JSON rubric; explicitly selectable legacy-rich mode preserves the production chronological tutorial.md with base64 images. Use when a user supplies a tutorial video or URL and wants reproducible steps, keyframes, exact parameters, or tutorial production.
- ▌ Bio Clinical Databases Somatic Signatures · freedomintelligence bundleExtract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes. Use when identifying DNA damage mechanisms or etiology in cancer genomes.
- ▌ Bio Causal Genomics Colocalization Analysis · freedomintelligence bundleTest whether two traits share a causal variant at a genomic locus using Bayesian colocalization with coloc. Computes posterior probabilities for shared vs distinct causal variants between GWAS and eQTL signals. Use when determining if a GWAS signal and an eQTL share the same causal variant.
- ▌ Bio Causal Genomics Mendelian Randomization · freedomintelligence bundleEstimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR. Implements IVW, MR-Egger, weighted median, and MR-PRESSO methods for robust causal inference from GWAS summary statistics. Use when testing whether an exposure causally affects an outcome using genetic instruments.
- ▌ Bio Variant Calling Filtering Best Practices · freedomintelligence bundleComprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels. Use when filtering variants using GATK best practices.
- ▌ Bio Gatk Variant Calling · freedomintelligence bundleVariant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use when calling variants with GATK HaplotypeCaller.
- ▌ Bio Reaction Enumeration · freedomintelligence bundleEnumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries from building blocks using defined chemical reactions with product validation. Use when creating combinatorial libraries or enumerating products from synthetic routes.
- ▌ Bio Similarity Searching · freedomintelligence bundlePerforms molecular similarity searches using Tanimoto coefficient on fingerprints via RDKit. Finds structurally similar compounds using ECFP or MACCS keys and clusters molecules by structural similarity using Butina clustering. Use when finding analogs of a query compound or clustering chemical libraries.
- ▌ Bio Alignment Msa Parsing · freedomintelligence bundleParse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.
- ▌ Bio Chipseq Visualization · freedomintelligence bundleVisualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions. Use when visualizing ChIP-seq signal and peaks.
- ▌ Bio Methylation Methylkit · freedomintelligence bundleDNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comparing samples, or preparing data for DMR detection.
- ▌ Bio Pathway Go Enrichment · freedomintelligence bundleGene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression or other analyses. Supports all three ontologies (BP, MF, CC), multiple ID types, and customizable statistical thresholds.
- ▌ Bio Pathway Kegg Pathways · freedomintelligence bundleKEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a gene list. Supports 4000+ organisms via KEGG online database.
- ▌ Bio Chipseq Peak Annotation · freedomintelligence bundleAnnotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. Find nearest genes and calculate distance to TSS. Generate annotation plots and statistics. Use when annotating ChIP-seq peaks to genomic features.
- ▌ Bio Alignment Msa Statistics · freedomintelligence bundleCalculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.
- ▌ Bio Atac Seq Motif Deviation · freedomintelligence bundleAnalyze transcription factor motif accessibility variability using chromVAR. Use when identifying which TF motifs show variable accessibility across samples or conditions in ATAC-seq data.
- ▌ Bio Methylation Dmr Detection · freedomintelligence bundleDifferentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation differences between experimental conditions or cell types.
- ▌ Bio Variant Calling Deepvariant · freedomintelligence bundleDeep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data. Use when calling variants with DeepVariant deep learning caller.
- ▌ Bio Causal Genomics Fine Mapping · freedomintelligence bundleIdentify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Computes posterior inclusion probabilities and credible sets to prioritize variants for functional follow-up. Use when narrowing GWAS association signals to candidate causal variants or building credible sets for functional validation.
- ▌ Bio Methylation Bismark Alignment · freedomintelligence bundleBisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.
- ▌ Bio Causal Genomics Mediation Analysis · freedomintelligence bundleDecompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing whether a molecular phenotype mediates the genotype-to-phenotype relationship.
- ▌ Ukb Navigator · freedomintelligence bundleSemantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.
- ▌ Bio Alignment Io · freedomintelligence bundleRead, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
- ▌ Bio Pathway Gsea · freedomintelligence bundleGene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coordinated expression changes in gene sets without arbitrary significance cutoffs. Detects subtle but coordinated expression changes.
- ▌ Pharmgx Reporter · freedomintelligence bundlePharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs
- ▌ Claw Semantic Sim · freedomintelligenceSemantic Similarity Index for disease research literature using PubMedBERT embeddings
- ▌ Scrna Orchestrator · freedomintelligence bundleLocal Scanpy pipeline for single-cell RNA-seq QC, clustering, marker discovery, and optional two-group differential expression from raw-count .h5ad.
- ▌ Bio Variant Calling · freedomintelligence bundleCall SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.
- ▌ Bio Pathway Reactome · freedomintelligence bundleReactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database. Performs over-representation analysis and GSEA with visualization and pathway hierarchy exploration.
- ▌ Bio Isoform Switching · freedomintelligence bundleAnalyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain changes, NMD sensitivity, ORF alterations, and coding potential shifts between conditions. Use when investigating how splicing changes affect protein function.
- ▌ Bio Consensus Sequences · freedomintelligence bundleGenerate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.
- ▌ Bio Substructure Search · freedomintelligence bundleSearches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functional groups, or scaffold matches with atom mapping. Use when finding compounds containing specific chemical moieties or filtering libraries by structural features.
- ▌ Gwas Prs · freedomintelligence bundleCalculate polygenic risk scores from DTC genetic data using the PGS Catalog
- ▌ Gwas Lookup · freedomintelligence bundleFederated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.