Business & Operations

Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data.

Normalize indel representation, decompose MNPs, and split multiallelic variants using bcftools norm. Use when comparing variants from different callers, preparing VCF for database annotation, or merging VCFs from multiple sources.

Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.

Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experiments using ssizeRNA, PROPER, powsimR for scRNA-seq, and pilot-data dispersion estimation from DESeq2/edgeR. Covers the biological-versus-technical replication distinction (technical replicates do not add degrees of freedom for biological inference), replicate-number-versus-sequencing-depth budgeting, scRNA-seq sample-versus-cell allocation under a pseudobulk model, and the criti...

Create a workspace skeleton for a new project, client, or venture. Gathers details, creates directory with populated templates, validates generated files, populates dashboard, and updates main dashboard. Use when user says \"new workspace\", \"new project\", \"new client setup\".

End-of-session reflection generating persistent learnings about user preferences, communication patterns, and cross-session insights. Activates when wrapping up a session, or when user says \"let's wrap up\", \"end the session\", \"time to reflect\", or \"meditate\". Also extracts judgment rules from decisions made during the session. See also: `weekly-review` and `growth-check` for time-based reflection cadences.

Process multiple source documents with Extract-Then-Aggregate discipline. Use when user shares multiple transcripts, emails, or documents for batch processing. See also: `capture-meeting` for a single meeting transcript; `file-document` for a single document; `summarize-doc` when you only need a summary.

DolphinDB data import guide for IoT and general scenarios. Covers CSV/TXT, JSON, binary, plugin-based (HDF5, Parquet, MySQL, ODBC), and IoT real-time ingestion (MQTT, OPC UA). Includes IOTDB engine, date/time conversion, array vector import, null handling, and binary record import. Does NOT cover database administration, permission management, stream compute engine configuration, or data export.

Use this skill when the user wants to manage kanban boards, project tasks, sprints, or todo items — or when they need a shared visual board that both humans and AI agents can update.

Use this skill when the user needs help with French bureaucracy, accounting, tax, notary, audit, property management, or any French administrative paperwork.

Use this skill when the user wants to manage Linear issues, projects, teams, and workflows from the command line using the Linear API.

Use this skill when the user wants to manage personal or business finances via plain text accounting — check balances, view transaction history, list accounts, or generate financial reports.

Computes immune-repertoire diversity, clonal structure, overlap, and segment usage from TCR/BCR clonotype tables with VDJtools (immunarch as the modern R alternative). Use when deciding which diversity estimator answers a question (q=0 observed richness/chao1/chaoE, q=1 shannonWienerIndex, q=2 inverseSimpson as a Hill profile); normalizing sequencing depth before any cross-sample claim (DownSample or the resampled CalcDiversityStats table); choosing an overlap metric (depth-robust MorisitaHor...

Runs all-in-one FASTQ preprocessing with fastp in a single pass - adapter trimming via paired-end overlap analysis, quality/length filtering, 2-color poly-G removal, base correction, optional dedup/UMI/merge, and HTML/JSON reports. Use when preprocessing bulk Illumina data and wanting one fast tool instead of separate Cutadapt, Trimmomatic, and FastQC steps. For precise small-RNA/amplicon adapters use adapter-trimming; for molecule-accurate UMI dedup use umi-processing.

Tests a gene list (ORA, enrichWP) or a ranked gene vector (GSEA, gseWP) against the WikiPathways community-curated pathway collection with clusterProfiler and rWikiPathways. Covers why a WikiPathways result is a snapshot of a live, monthly-updated database (enrichWP/gseWP/gson_WP silently pull data.wikipathways.org/current/), why reproducibility requires pinning a dated GMT via downloadPathwayArchive(date=, format='gmt'), why the WP GMT is Entrez-keyed so symbols and Ensembl silently overlap ...

Runs Gene Ontology over-representation analysis (ORA) on a gene LIST with clusterProfiler enrichGO, the one-sided hypergeometric/Fisher 2x2 test phyper(k-1, M, N-M, n, lower.tail=FALSE). Covers why the BACKGROUND universe (not the gene list) is the null and decides significance, why omitting universe= is a bug, why enrichGO defaults to ont='MF' not 'BP', why pvalueCutoff filters p.adjust not raw p, why ORA discards effect magnitude and inherits GO-DAG true-path redundancy (simplify, topGO), w...

Turns an enrichResult or gseaResult from clusterProfiler/enrichplot into a figure that collapses or shows gene-set redundancy, using dotplot, barplot, cnetplot, emapplot, treeplot, ridgeplot, gseaplot2, and upsetplot. Covers why a default top-20 GO dotplot is one biological theme drawn twenty times (the DAG/nesting guarantees redundant overlapping terms), so the figure is a modeling choice between SHOWING redundancy (pairwise_termsim -> emapplot/treeplot) and DELETING it (simplify/REVIGO); wh...

Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experiments using ssizeRNA, PROPER, powsimR for scRNA-seq, and pilot-data dispersion estimation from DESeq2/edgeR. Covers the biological-versus-technical replication distinction (technical replicates do not add degrees of freedom for biological inference), replicate-number-versus-sequencing-depth budgeting, scRNA-seq sample-versus-cell allocation under a pseudobulk model, and the criti...

Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critiq...

Detect distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence identity falls into the twilight zone (<35% pairwise), when BLAST fails to find homologs that should exist, when working at metagenomic scale (DIAMOND, MMseqs2), or when structure beats sequence (Foldseek). Covers PSI-BLAST (iterative PSSM), jackhmmer (iterative HMM), HHblits/HHsearch (profile-profile), DIAMOND, MMseqs2, and Foldseek (3Di structural alphabet, van Kempen 2024).

Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than rel...

Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.

Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying...

Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.