188 skills (repositories by FreedomIntelligence) · sorted by popularity
Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testing for significant changes in cell frequencies or marker expression between groups.
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Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods. Use when filtering out cell aggregates before clustering or quantitative analysis.
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Read and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loading and inspecting flow or mass cytometry data before preprocessing.
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Manual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates. Use when identifying cell populations through hierarchical gating strategies.
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Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.
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Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fragment ratios, and DELFI-style fragmentation profiles for cancer detection. Use when leveraging fragment patterns for tumor detection or tissue-of-origin analysis.
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Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positions for C-to-T or A-to-G conversions without double-strand breaks. Use when designing base editor experiments for precise nucleotide changes.
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Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats. Use when loading or converting Hi-C contact matrices.
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Variant 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.
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CRISPR library design for genetic screens. Covers sgRNA selection, library composition, control design, and oligo ordering. Use when designing custom sgRNA libraries for knockout, activation, or interference screens.
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Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes. Use when identifying significant genes from screen count data after QC passes.
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Detect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and germline CNV calling. Use when detecting CNVs from WES or targeted panel sequencing data.
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Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discovering cell populations in high-dimensional cytometry data without predefined gates.
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Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when filtering and exporting DE analysis results.
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Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis. Use when identifying candidate disease-causing variants from exome or genome sequencing.
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Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms. Use when correcting spectral overlap between fluorophores or transforming data for analysis.
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Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns. Use when screening genomes for AMR genes or tracking resistance in surveillance programs.
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Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices. Use when identifying A/B compartments from Hi-C data.
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Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.
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Query gnomAD for population allele frequencies to assess variant rarity. Use when filtering variants by population frequency for rare disease analysis or determining if a variant is common in the general population.
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Parse 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.
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Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies.
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End-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) Want high experimental success rate. For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-qc. For tool selection guidance, use binder-design.
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Predicts ADMET properties using ADMETlab 3.0 API or DeepChem models. Estimates bioavailability, CYP inhibition, hERG liability, and 119 toxicity endpoints with uncertainty quantification. Filters for PAINS and other structural alerts. Use when filtering compounds for drug-likeness or prioritizing leads by predicted safety.
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