14,555 skills found ¡ Page 196 of 486
FreedomIntelligence / bio-immunoinformatics-immunogenicity-scoringScore and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features. Rank candidates for vaccine design
FreedomIntelligence / bio-immunoinformatics-mhc-binding-predictionPredict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from protein sequences
FreedomIntelligence / bio-immunoinformatics-neoantigen-predictionIdentify tumor neoantigens from somatic mutations using pVACtools for personalized cancer immunotherapy. Predict mutant peptides that bind patient HLA and may elicit T-cell responses
FreedomIntelligence / bio-immunoinformatics-tcr-epitope-bindingPredict TCR-epitope specificity using ERGO-II and deep learning models for T-cell receptor antigen recognition. Match TCRs to their cognate epitopes or predict TCR targets
FreedomIntelligence / bio-cfdna-preprocessingPreprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering
FreedomIntelligence / alphafoldValidate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain câĻ
FreedomIntelligence / arboretoInfer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3)
FreedomIntelligence / arxiv-searchSearch arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic search.
FreedomIntelligence / bindcraftEnd-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5)âĻ
FreedomIntelligence / binder-designGuidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types.
FreedomIntelligence / bio-alignment-filteringFilter alignments by flags, quality, and regions using samtools and pysam.
FreedomIntelligence / bio-alignment-indexingCreate indices for random access to alignment files using samtools and pysam.
FreedomIntelligence / bio-alignment-pairwisePerform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner
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-atac-seq-atac-peak-callingCall accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters
FreedomIntelligence / bio-atac-seq-differential-accessibilityFind differentially accessible chromatin regions between conditions using DiffBind or DESeq2
FreedomIntelligence / bio-atac-seq-footprintingDetect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS
FreedomIntelligence / bio-atac-seq-motif-deviationAnalyze transcription factor motif accessibility variability using chromVAR
FreedomIntelligence / bio-atac-seq-nucleosome-positioningExtract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis
FreedomIntelligence / bio-batch-downloadsDownload large numbers of records from NCBI efficiently using the history server, batching, and proper rate limiting.
FreedomIntelligence / bio-blast-searchesRun BLAST searches against NCBI databases using Biopython's Bio.Blast module.
FreedomIntelligence / bio-chipseq-super-enhancersIdentifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools
FreedomIntelligence / bio-clinical-databases-clinvar-lookupQuery ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF
FreedomIntelligence / bio-clinical-databases-gnomad-frequenciesQuery gnomAD for population allele frequencies to assess variant rarity
FreedomIntelligence / bio-clinical-databases-hla-typingCall HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications
FreedomIntelligence / bio-clinical-databases-myvariant-queriesQuery myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request
FreedomIntelligence / bio-clinical-databases-pharmacogenomicsQuery PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines
FreedomIntelligence / bio-clinical-databases-polygenic-riskCalculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics
FreedomIntelligence / bio-clinical-databases-tumor-mutational-burdenCalculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds
