Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant.
Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment.
Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment.
Detect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation, identifying pause sites, or analyzing codon — from…
Detect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation, identifying pause sites, or analyzing codon — from…
Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between conditions or identifying — from…
Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between conditions or identifying — from…
Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto. — from bg-szy/TOP-SKILLS
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta.
Searches for non-coding RNA homologs and classifies RNA families using Infernal covariance model searches against the Rfam database.
RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage, and transcript integrity metrics.
RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage, and transcript integrity metrics.
Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H — from…
Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H — from…
Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy.
Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy.
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData.
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData.
Estimate cell type composition in spatial transcriptomics spots using reference-based deconvolution. Use cell2location, RCTD, SPOTlight, or Tangram to infer cell type pro — from…
Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy.
Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy.
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.
Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay triangulation, and radius-based connectivity for downs — from…
Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay triangulation, and radius-based connectivity for downs — from…
Quality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics, filter spots/cells, normalize counts, and identif — from…
Quality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics, filter spots/cells, normalize counts, and identif — from…
Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization.
Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization.
Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autocorrelation, co-occurrence analysis, and neighborho — from…
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images.
Quantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-turbo from BAM files.
Transcribe DNA to RNA and translate to protein using Biopython. Use when converting between DNA, RNA, and protein sequences, finding ORFs, or using alternative codon tabl — from…
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical sig — from…
Generate reproducible bioinformatics/data-science Methods + run documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including a top-of-doc workflow summary, exact…
End-to-end pooled and single-cell CRISPR screen analysis from FASTQ to hit genes. Orchestrates library design QC, guide counting, six-stage screen QC (plasmid Gini, replicate…
End-to-end gene regulatory network inference pipeline from processed single-cell data to regulon discovery and perturbation simulation.
Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware genome…
End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcripto — from…
End-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation. — from bg-szy/TOP-SKILLS
End-to-end spatial transcriptomics workflow for Visium/Xenium data. Covers data loading, preprocessing, spatial analysis, domain detection, and visualization with Squidpy — from…
Use when implementing data analysis pipelines, statistical tests, or bioinformatics workflows in code (Python/R), particularly for genomics, transcriptomics, proteomics, or other…
Use biotech-pitch-deck-narrative for academic writing workflows that need structured investor-facing storytelling, explicit assumptions, and clear output boundaries.
Claude'a herhangi bir videoyu izleme yeteneği kazandıran skill — yt-dlp ile indirir, ffmpeg ile frame çeker, transcript alır, Claude'a iletir. /watch komutu ile çalışır.
Hyperframes-based video template for retro pixel deck motion design. Use when users want a high-fidelity, multi-scene HTML-to-video composition with advanced transitions — from…
Use when defining a new role in Bknd authorization system. Covers role properties (implicit_allow, is_default, permissions), permission assignment, role hierarchies, and common…
Adds a complete blog feature to an existing Blazor WebAssembly Static Web App with Azure Functions backend and Azure File Share for markdown storage.
React editor components for WordPress blocks in Oh My Brand! theme. useBlockProps, InspectorControls, MediaUpload, and attributes. Use when writing edit.tsx files.
Copy-paste scaffolds for Oh My Brand! blocks. Templates for block.json, render.php, helpers.php, view.ts, style.css, and tests. Use when creating new blocks.
Work with BlockNote, a block-based rich text editor for React. Use when the user mentions "blocknote", "BlockNote editor", "block-based editor", "insertBlocks", "updateBlock",…
Create a new technical blog post with deep educational value and professional quality
Review and improve the blog post draft for clarity, engagement, and authentic voice.
Track blog post performance and generate insights for continuous improvement. USE WHEN user says 'track post performance', 'analyze blog metrics', 'what posts performed well',…
Complete workflow for creating and publishing blog articles with Claude AI and WordPress MCP integration.
Complete blog article creation workflow with automatic OG image generation. Use for creating new blog articles - supports prime (research), plan, execute, validate, and…
Use when managing blog-cc static sites - content creation, deployment, themes, courses. Conversational content management with AI generation, validation, and GitHub Pages…
Generate dark-mode-compatible inline SVG data visualization charts for blog posts. Supports horizontal bar, grouped bar, donut, line, lollipop, area, and radar charts with…
Create/update Markdown blog posts and topic metadata for this Next.js static-export blog (multi-language en/tr).
Use when the user asks to generate a blog cover image, thumbnail, or article header. Automatically uses modern typography, brand logos, and Google Search grounding to cre — from…
Use when the user asks to generate a blog cover image, thumbnail, or article header. Automatically uses modern typography, brand logos, and Google Search grounding to cre — from…