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Showing 9,121–9,180 of 13,471 skills · Page 153 of 225
microsoft / microsoft-docs
3.1kUnderstand Microsoft technologies by querying official documentation
microsoft / podcast-generation
3.1kGenerate AI-powered podcast-style audio narratives using Azure OpenAI's GPT Realtime Mini model via WebSocket
microsoft / azure-ai-language-conversations-py
3.1kImplement Conversational Language Understanding (CLU) using the azure-ai-language-conversations Python SDK
microsoft / azure-app-onboard-prereq
3.1kAssess whether source code is ready to deploy to Azure — the check BEFORE infrastructure work. Evaluates build health, app completeness, dependencies and local services, stack compatibility, and deployment feasibility.
microsoft / azure-kubernetes
3.1kPlan, create, and configure production-ready Azure Kubernetes Service (AKS) clusters. Covers Day-0 checklist, SKU selection (Automatic vs Standard), networking options (private API server, Azure CNI Overlay, egress configuration), security, and operations (autoscaling, upgrade strategy, cost analysi…
microsoft / azure-resource-visualizer
3.1kAnalyze Azure resource groups and generate detailed Mermaid architecture diagrams showing the relationships between individual resources.
microsoft / azure-upgrade
3.1kAssess and upgrade Azure workloads between plans, tiers, or SKUs, or modernize Azure SDK dependencies in source code. WHEN: upgrade Consumption to Flex Consumption, upgrade Azure Functions plan, change hosting plan, function app SKU, migrate App Service to Container Apps, modernize legacy Azure Java…
microsoft / entra-app-registration
3.1kGuides Microsoft Entra ID app registration, OAuth 2.0 authentication, and MSAL integration. USE FOR: create app registration, register Azure AD app, configure OAuth, set up authentication, add API permissions, generate service principal, MSAL example, console app auth, Entra ID setup, Azure AD authe…
microsoft / wiki-llms-txt
3.1kGenerates llms.txt and llms-full.txt files for LLM-friendly project documentation following the llms.txt specification
FreedomIntelligence / alphafold
3.0kValidate 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 c…
FreedomIntelligence / arboreto
3.0kInfer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3)
FreedomIntelligence / arxiv-search
3.0kSearch arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic search.
FreedomIntelligence / bindcraft
3.0kEnd-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)…
FreedomIntelligence / binder-design
3.0kGuidance 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-filtering
3.0kFilter alignments by flags, quality, and regions using samtools and pysam.
FreedomIntelligence / bio-alignment-indexing
3.0kCreate indices for random access to alignment files using samtools and pysam.
FreedomIntelligence / bio-alignment-pairwise
3.0kPerform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner
FreedomIntelligence / bio-alignment-sorting
3.0kSort alignment files by coordinate or read name using samtools and pysam.
FreedomIntelligence / bio-alignment-validation
3.0kPost-alignment quality control to verify alignment quality and identify issues.
FreedomIntelligence / bio-atac-seq-atac-peak-calling
3.0kCall accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters
FreedomIntelligence / bio-atac-seq-differential-accessibility
3.0kFind differentially accessible chromatin regions between conditions using DiffBind or DESeq2
FreedomIntelligence / bio-atac-seq-footprinting
3.0kDetect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS
FreedomIntelligence / bio-atac-seq-motif-deviation
3.0kAnalyze transcription factor motif accessibility variability using chromVAR
FreedomIntelligence / bio-atac-seq-nucleosome-positioning
3.0kExtract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis
FreedomIntelligence / bio-batch-downloads
3.0kDownload large numbers of records from NCBI efficiently using the history server, batching, and proper rate limiting.
FreedomIntelligence / bio-blast-searches
3.0kRun BLAST searches against NCBI databases using Biopython's Bio.Blast module.
FreedomIntelligence / bio-chipseq-super-enhancers
3.0kIdentifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools
FreedomIntelligence / bio-clinical-databases-clinvar-lookup
3.0kQuery ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF
FreedomIntelligence / bio-clinical-databases-gnomad-frequencies
3.0kQuery gnomAD for population allele frequencies to assess variant rarity
FreedomIntelligence / bio-clinical-databases-hla-typing
3.0kCall HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications
FreedomIntelligence / bio-clinical-databases-myvariant-queries
3.0kQuery myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request
FreedomIntelligence / bio-clinical-databases-pharmacogenomics
3.0kQuery PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines
FreedomIntelligence / bio-clinical-databases-polygenic-risk
3.0kCalculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics
FreedomIntelligence / bio-clinical-databases-tumor-mutational-burden
3.0kCalculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds
FreedomIntelligence / bio-clinical-databases-variant-prioritization
3.0kFilter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis
FreedomIntelligence / bio-clip-seq-clip-peak-calling
3.0kPureCLIP uses an HMM to model crosslink sites, incorporating enrichment and truncation signals.
FreedomIntelligence / bio-codon-usage
3.0kAnalyze codon usage patterns and calculate codon adaptation metrics using Biopython.
FreedomIntelligence / bio-compressed-files
3.0kRead and write compressed sequence files (gzip, bzip2, BGZF) using Biopython
FreedomIntelligence / bio-consensus-sequences
3.0kGenerate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus
FreedomIntelligence / bio-copy-number-cnv-annotation
3.0kAnnotate CNVs with genes, pathways, and clinical significance
FreedomIntelligence / bio-crispr-screens-jacks-analysis
3.0kJACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality
FreedomIntelligence / bio-data-visualization-circos-plots
3.0kCircular genome visualizations for displaying multiple data tracks around chromosome ideograms.
FreedomIntelligence / bio-entrez-fetch
3.0kRetrieve records from NCBI databases using Biopython's Entrez module (EFetch, ESummary utilities).
FreedomIntelligence / bio-entrez-link
3.0kNavigate between NCBI databases using Biopython's Entrez module (ELink utility).
FreedomIntelligence / bio-entrez-search
3.0kSearch NCBI databases using Biopython's Entrez module (ESearch, EInfo, EGQuery utilities).
FreedomIntelligence / bio-filter-sequences
3.0kFilter and select sequences by criteria (length, ID, GC content, patterns) using Biopython
FreedomIntelligence / bio-flow-cytometry-compensation-transformation
3.0kSpillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms
FreedomIntelligence / bio-flow-cytometry-differential-analysis
3.0kDifferential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods
FreedomIntelligence / bio-flow-cytometry-fcs-handling
3.0kRead and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration
FreedomIntelligence / bio-flow-cytometry-gating-analysis
3.0kManual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates
FreedomIntelligence / bio-genome-assembly-assembly-polishing
3.0kImprove assembly accuracy by correcting errors using additional sequencing data.
FreedomIntelligence / bio-genome-assembly-assembly-qc
3.0kEvaluate genome assembly quality with contiguity metrics (QUAST) and gene completeness (BUSCO).
FreedomIntelligence / bio-genome-assembly-long-read-assembly
3.0kAssemble genomes from Oxford Nanopore (ONT) or PacBio long reads for highly contiguous assemblies.
FreedomIntelligence / bio-genome-assembly-short-read-assembly
3.0kAssemble genomes from Illumina paired-end or single-end reads using SPAdes.
FreedomIntelligence / bio-genome-intervals-bed-file-basics
3.0kBED (Browser Extensible Data) format stores genomic intervals. Uses 0-based, half-open coordinates.
FreedomIntelligence / bio-genome-intervals-bigwig-tracks
3.0kBigWig is an indexed binary format for continuous genomic data. Efficient for genome browsers and programmatic access.
FreedomIntelligence / bio-genome-intervals-coverage-analysis
3.0kCalculate coverage and depth across genomic regions using bedtools and pybedtools.
FreedomIntelligence / bio-genome-intervals-gtf-gff-handling
3.0kGTF and GFF3 are standard gene annotation formats. Both use 1-based coordinates.
FreedomIntelligence / bio-genome-intervals-interval-arithmetic
3.0kCore set operations on genomic intervals using bedtools (CLI) and pybedtools (Python).
FreedomIntelligence / bio-genome-intervals-proximity-operations
3.0kOperations for finding nearby features and extending intervals using bedtools and pybedtools.