Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC.
Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing figures for journal submission, creating vector gr — from…
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships.
Count reads per gene from aligned BAM files using Subread featureCounts. Use when processing BAM files from STAR/HISAT2 to generate gene-level counts for DESeq2/edgeR.
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignmen — from…
Find homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis.
Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations.
Discover novel miRNAs and quantify known miRNAs using miRDeep2 de novo prediction from small RNA-seq data.
Fast miRNA quantification with isomiR detection and A-to-I editing analysis using miRge3. Use when quantifying known miRNAs quickly or analyzing isomiR variants and RNA e — from…
Preprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs.
Predict miRNA target genes using sequence-based algorithms and database lookups. Use when identifying potential mRNA targets of differentially expressed or functionally i — from…
End-to-end alternative splicing analysis from FASTQ to differential splicing results. Aligns with STAR 2-pass mode, performs junction QC, runs rMATS-turbo for differentia — from…
Download sequencing data from NCBI SRA using the SRA toolkit. Use when downloading FASTQ files from SRA accessions, prefetching large datasets, or validating SRA downloads.
Access UniProt protein database for sequences, annotations, and functional information. Use when retrieving protein data, GO terms, domain annotations, or protein-protein…
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical sig — from…
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments. — from bg-szy/TOP-SKILLS
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data.
Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels.
Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR.
Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that — from…
Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream ana — from…
View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structu — from…
Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data. — from bg-szy/TOP-SKILLS
End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection with Boruta/LASSO, classifier training with nested CV — from…
End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker.
End-to-end CLIP-seq analysis from FASTQ to binding sites and motif enrichment. Use when analyzing protein-RNA interactions from CLIP-based methods. — from bg-szy/TOP-SKILLS
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation.
Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization.
End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCa — from…
End-to-end Hi-C analysis workflow from contact pairs to compartments, TADs, and loops. Covers cooler matrices, cooltools analysis, and visualization.
End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV.
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profi — from…
End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit — from…
End-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality processing, and WNN integration with Seurat/Signac.
End-to-end neoantigen discovery from somatic variants to ranked vaccine candidates. Integrates HLA typing, MHC binding prediction, pVACtools neoantigen calling, and immun — from…
End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission infer — from…
End-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visual — from…
End-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation — from…
End-to-end small RNA-seq analysis from FASTQ to differential miRNA expression. Use when analyzing miRNA, piRNA, or other small RNA sequencing data. — from bg-szy/TOP-SKILLS
End-to-end somatic variant calling from tumor-normal paired samples using Mutect2 or Strelka2. Covers preprocessing, variant calling, filtering, and annotation for cancer — from…
Open source biomedical Model Context Protocol (MCP) toolkit for connecting LLMs to biomedical data sources (PubMed, ClinicalTrials, Genomics).
bkend.ai authentication — email/social login, JWT tokens, RBAC, session management. Triggers: bkend auth, login, signup, JWT, RBAC, 인증, 로그인, 회원가입.
bkend.ai project tutorials (todo to SaaS) and common error troubleshooting. Triggers: bkend tutorial, cookbook, troubleshooting, 튜토리얼, 에러 해결.
bkend.ai database — CRUD, column types, filtering, sorting, relations, indexing. Triggers: bkend table, CRUD, column, filter, sort, relation, 테이블, 데이터.
bkend.ai MCP tools and AI integration expert skill. Covers 28 MCP tools (Fixed 3 + Project 6 + Table 9 + Data CRUD 5 + Env 3 + Schema 2), 4 MCP resources, OAuth 2.1 + PKCE…
bkend.ai onboarding — MCP setup, resource hierarchy, tenant/user model, first project. Triggers: bkend quickstart, onboarding, setup, MCP, 시작하기, 온보딩.
bkend.ai file storage — upload (presigned URL), download (CDN), visibility levels, buckets. Triggers: bkend file, upload, download, presigned URL, storage, 파일 업로드, 스토리지.
Core rules for bkit — PDCA methodology, level detection, agent triggering, quality standards. Triggers: bkit rules, core rules, methodology, 핵심 규칙, PDCA 규칙.
PDCA document templates — Plan, Design, Analysis, Report with consistent structure. Triggers: template, plan document, design template, 템플릿, 문서 양식.
Remove signs of AI-generated writing from text. Use when editing or reviewing text to make it sound more natural and human-written.
Brain-aware blame on a file or file:line. Combines git blame (who/when/commit) with the brain (which intent introduced this work, decisions affecting the file, recent edits log).
BLAST skill for sequence similarity searching, homology detection, and database querying
Integracao com BMAD Method para escala adaptativa e workflows guiados. Detecta nivel de complexidade e ajusta agentes automaticamente.
AI-powered bone marrow morphology analysis, cell classification, and hematologic disorder diagnosis using deep learning on aspirate and biopsy images.
Analyze a folder of books and audiobooks: scan it, identify every book (author + title), enrich each with web data (year, genre, tags, short description, Goodreads rating), save a…
Apply BOUCH voice rules to any UK business copy: websites, emails, proposals, case studies, or LinkedIn. Covers language to use and avoid, tone, British spelling, and formatting.
Serves the user a random TikTok with brainrot commentary before starting any work. Auto-fires before every task per CLAUDE.md persona rules. Can also be invoked manually.
The CLARIFYING phase discusses each item one at a time to fully understand requirements
The EXPLORING phase gathers context about the project and forms an initial understanding
The VALIDATING phase runs the completeness gate to ensure design is ready for implementation