Productivity

holobiomicslab Skill

Use when you have raw LC-MS data (mzML, NetCDF) from multiple runs that require sequential feature detection, alignment, quantification, and optional filtering (e.g., blank exclusion, QC reproducibility, retention-time outlier removal) before spatial mapping or annotation.

holobiomicslab Skill

Use when you have raw or partially processed metabolomics data (mzML/mzXML format) from LC-MS or GC-MS runs and need to apply standardized feature detection, alignment, and intensity normalization as part of a reproducible workflow.

holobiomicslab Skill

Use when after parent chemical suspects have been identified in a non-target screening workflow, use this skill when you need to screen for downstream products formed by chemical or biological transformation.

holobiomicslab Skill

Use when when you have a collection of mzML.gz files from a multidimensional MS instrument (e.

netvar1337 Bundle

Use for authorized multi-stage attack-path planning and orchestration when a task spans reconnaissance, initial access, privilege escalation, lateral movement, or impact assessment. Route single-stage tasks directly to their specialist skill.

netvar1337 Skill

Use for GitHub PR lifecycle: branch, commit, open, CI, merge.

holobiomicslab Skill

Use when you have multiple pre-trained neural network models (e.g., MLP and GNN) that produce overlapping predictions on the same set of candidates, and your evaluation metric is rank-based (average rank, Rank@K) rather than point-wise accuracy or RMSE.

holobiomicslab Skill

Use when you have acquired imaging mass spectrometry (IMS) data stored in imzML format (accompanied by an .ibd ion binary data file) and need to load it into a Python-based spatial metabolomics workflow.

holobiomicslab Skill

Use when you have generated a lipid spectral library (with lipid identities, adducts, m/z values, and fragmentation patterns) and need to export it for downstream mass spectrometry analysis on either an Orbitrap (via Excalibur DDA) or via Skyline's transition-based workflow.

holobiomicslab Skill

Use when after invoking the DEIMoS CLI with a configuration file and allowing the Snakemake workflow to execute, use this skill to confirm successful completion of all workflow rules.

holobiomicslab Skill

Use when when converting pre-processed MS/MS spectra into fixed-length vector representations using Word2Vec embeddings for Spec2Vec similarity scoring. Specifically, apply this skill after you have represented individual peaks and neutral losses as words ('[redacted-email]', 'loss@xxx.

holobiomicslab Skill

Use when when you have imzML mass spectrometry imaging data files and need to convert raw ion image intensities into quantitative lipid abundance (pmol/mm²) using known internal standards.

holobiomicslab Skill

Use when you have raw CE-MS or LC-MS instrument files (stored as OnDiskMSnExp objects or similar Bioconductor containers) and need to extract quantitative features (migration times, m/z values, peak intensities) by orchestrating multiple R packages in a controlled, documented sequence.

holobiomicslab Skill

Use when when evaluating whether an MS data processing platform (such as mzmine) supports the full range of separation/ionization techniques your laboratory uses, or when assessing whether gaps exist in the software architecture that would require external pre- or post-processing for specific.

holobiomicslab Skill

Use when when you have received chemical annotations from GNPS spectral library matching workflow and need to assess their reliability before downstream analysis (e.g., chemical explorer visualization, sample filtering, or comparative metabolomics).

intense-visions Bundle

Test TDD Workflow

holobiomicslab Skill

Use when you have a collection of mzML or mzML.gz files from LC-IMS-MS/MS experiments and need to apply a consistent, reproducible sequence of feature detection, alignment, CCS calibration, isotope detection, and MS/MS deconvolution operations across multiple samples.

holobiomicslab Skill

Use when after MS1 feature detection and spectra merging in an untargeted or semi-targeted metabolomics workflow, when you have a list of observed accurate m/z values from high-resolution mass spectrometry (e.

holobiomicslab Skill

Use when when you have centroided mzML files from LC-MS metabolomics and need to construct high-mass-resolution mass tracks for each sample before alignment. Apply this skill at the start of an untargeted metabolomics workflow, before building a cross-sample MassGrid.

jiayaoqijia Bundle

Acton CLI workflow for TON smart contract development in Tolk: install/update, project bootstrap, Acton.toml configuration, build/compile/wrapper generation, tests with coverage/gas/fuzz/mutation/UI, scripts and deployment, wallets, verification, RPC inspection, libraries, lint/format/hooks, LSP/completions, and troubleshooting.

jiayaoqijia Bundle

Multi-Step Workflows

jiayaoqijia Bundle

End-to-end limit order workflow with preflight checks, dry-run, placement, monitoring, amend, and cancel.

jiayaoqijia Bundle

Description

jiayaoqijia Bundle

Use this skill whenever the user wants to check prices, manage account balances, place or cancel orders, manage futures or spot positions, set leverage, transfer funds, check funding rates, use demo/paper trading, or do anything else on the Bitget exchange. Invoke this skill even when the user doesn't say "Bitget" by name — action phrases like "check my open orders", "cancel my BTC position", "move USDT to futures", "what's my P&L", "place a market sell", "how much can I withdraw", "show my positions", "set leverage to 10x", "what's the funding rate" all require this skill. Also invoke for Chinese-language trading requests such as "查看我的账户", "下一个限价单", "查看持仓盈亏", "转账到合约账户", "BTC现在多少钱" — these are Bitget operations even without the exchange name. Always invoke this skill before attempting any exchange trading task from scratch.

jiayaoqijia Bundle

Reproduce TON bugs on a local tontester network. Use only when the task involves launching tontester validators, deploying contracts to a local network, or comparing patched validator builds — not for general TON development or testnet interaction.

theneoai Bundle

A world-class podcast producer specializing in show concept development, episode production workflow, interview preparation, audio editing (noise reduction, EQ, compression, normalization), show Use when: media, podcast, audio-production, content-strategy, interview.

jiayaoqijia Bundle

Git workflow automation skill for commit message generation, branch management, pre-commit checks, and change history analysis

jiayaoqijia Bundle

Macro-economic and cross-asset analysis for crypto market context. Use this skill whenever the user asks about the broader economic environment and its effect on crypto or risk assets. Triggers include: macro outlook, interest rates, Fed policy, rate cut, rate hike, FOMC, yield curve, inverted yield curve, recession risk, inflation, CPI, PCE, jobs data, unemployment, GDP, 10-year yield, 2-year yield, spread, dollar strength, DXY, risk-on, risk-off, gold correlation, BTC vs S&P, cross-asset correlation, global markets, tech earnings impact on crypto, forex rates, euro, yen, China market, A-shares, economic calendar, macro environment.

fridrichmethod Bundle

Authors portable, strongly-typed bioinformatics pipelines in the Common Workflow Language (CWL v1.2) as CommandLineTool/Workflow/ExpressionTool documents, validated with cwltool and run at scale on Toil/Arvados/Calrissian. Use when deciding CWL (portability/provenance/regulated) vs Nextflow/WDL/Snakemake; declaring secondaryFiles for indexed companions (.bai/.fai/.dict/.tbi and the caret rule); putting resources/containers under requirements (must-hold) vs hints (advisory) to avoid silent OOM; choosing scatterMethod (dotproduct vs flat_/nested_crossproduct); preferring $(...) parameter refs over ${...} JavaScript for portability; pinning DockerRequirement images; or emitting a CWLProv provenance object for audited/clinical settings.

fridrichmethod Bundle

Use when you have a spec or requirements for a multi-step task, before touching code

fridrichmethod Bundle

Extracts UMIs and collapses reads to original molecules with umi_tools (directional dedup) or builds error-corrected single-strand/duplex consensus reads with fgbio. Use when the library has UMIs and accurate molecule counting or below-sequencer-floor error correction is needed - single-cell, low-input RNA-seq, targeted panels, and ctDNA/liquid-biopsy rare-variant detection. For UMI extraction during QC use fastp-workflow; do not dedup non-UMI bulk RNA-seq.

fridrichmethod Bundle

Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.

fridrichmethod Bundle

Removes sequencing adapters from FASTQ reads with Cutadapt and Trimmomatic, including paired-end read-through, small-RNA 3' adapters, amplicon primers, and anchored/linked adapters. Use when FastQC shows adapter content climbing toward the 3' end, when inserts are shorter than the read length (small-RNA, cfDNA, FFPE), or before assembly/k-mer analysis. For all-in-one trimming use fastp-workflow; for quality/length filtering use quality-filtering.

fridrichmethod Bundle

Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al. 2023), Pharmer / Pharmit for search, and PharmacoForge for protein-pocket-conditioned pharmacophore generation (Flynn et al. 2025), covering ligand-based pharmacophores from active-set alignment and receptor-based pharmacophores from binding-pocket geometry. Explicitly handles feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.

fridrichmethod Bundle

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.

fridrichmethod Bundle

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.