CLI Tools
Command line utilities
bio-chipseq-peak-calling
by GPTomics
ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats including narrowPeak and broadPeak BED files. Use when calling peaks from ChIP-seq alignments.
bio-alignment-files-bam-statistics
by GPTomics
Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.
bio-duplicate-handling
by GPTomics
Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
bio-sam-bam-basics
by GPTomics
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.
bio-alignment-sorting
by GPTomics
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
bioskills
by GPTomics
"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."
bio-alignment-filtering
by GPTomics
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
bio-atac-seq-atac-peak-calling
by GPTomics
Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
bio-chipseq-super-enhancers
by GPTomics
Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions that cluster into large enhancer domains.
shellck
by regenrek
Run shellcheck on shell scripts after editing scripts or when debugging shell errors. Use for linting scripts in a repo (especially scripts/), catching issues like set -u with unset vars, bad subshell usage, or quoting mistakes.
Bun Shell
by secondsky
Bun shell scripting with Bun.$, Bun.spawn, subprocess management. Use for shell commands, template literals, or command execution.
gh-repo-bootstrap
by regenrek
Create a new GitHub repository with the gh CLI and bootstrap a local project in ~/projects with git init, README, remote setup, and initial push. Use when the user asks to create a repo (public/private) in their account, set up the local folder, add the upstream remote, and push the first commit.
Bun Package Manager
by secondsky
Bun package manager commands (install, add, remove, update), workspaces, lockfiles, npm/yarn/pnpm migration. Use for dependency management with Bun.
Bun Test Basics
by secondsky
Use for bun:test syntax, assertions, describe/it, test.skip/only/each, and basic patterns.
Bun React SSR
by secondsky
Use when building server-rendered React with Bun, including streaming SSR, hydration, renderToString, or custom SSR without a framework.
app-store-deployment
by secondsky
Publishes mobile applications to iOS App Store and Google Play with code signing, versioning, and CI/CD automation. Use when preparing app releases, configuring signing certificates, or setting up automated deployment pipelines.
kalshi
by machina-sports
Kalshi prediction markets — events, series, markets, trades, and candlestick data. Public API, no auth required for reads. US-regulated exchange (CFTC). Covers soccer, basketball, baseball, tennis, NFL, hockey event contracts. Use when: user asks about Kalshi-specific markets, event contracts, CFTC-regulated prediction markets, or candlestick/OHLC price history on sports outcomes. Don't use when: user asks about actual match results, scores, or statistics — use football-data or fastf1 instead. Don't use for general "who will win" questions unless Kalshi is specifically mentioned — try polymarket first (broader sports coverage). Don't use for news — use sports-news instead.
web-search
by Memento-Teams
Web search and content fetching. Use when the user needs to search the web for information or fetch content from URLs.
nba-data
by machina-sports
NBA data via ESPN public endpoints — scores, standings, rosters, schedules, game summaries, play-by-play, win probability, injuries, transactions, futures, depth charts, team/player stats, leaders, and news. Zero config, no API keys. Use when: user asks about NBA scores, standings, team rosters, schedules, game stats, box scores, play-by-play, injuries, transactions, betting futures, depth charts, team/player statistics, or NBA news. Don't use when: user asks about WNBA (use wnba-data), college basketball (use cbb-data), or other sports.
nfl-data
by machina-sports
NFL data via ESPN public endpoints — scores, standings, rosters, schedules, game summaries, play-by-play, win probability, injuries, transactions, futures, depth charts, team/player stats, leaders, and news. Zero config, no API keys. Use when: user asks about NFL scores, standings, team rosters, schedules, game stats, box scores, play-by-play, injuries, transactions, betting futures, depth charts, team/player statistics, or NFL news. Don't use when: user asks about football/soccer (use football-data), college football (use cfb-data), or other sports.
by Memento-Teams
Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rotating pages, adding watermarks, creating new PDFs, filling PDF forms, encrypting/decrypting PDFs, extracting images, and OCR on scanned PDFs to make them searchable. If the user mentions a .pdf file or asks to produce one, use this skill.
polymarket
by machina-sports
Polymarket sports prediction markets — live odds, prices, order books, events, series, and market search. No auth required. Covers NFL, NBA, MLB, soccer, tennis, cricket, MMA, esports. Supports moneyline, spreads, totals, and player props. Use when: user asks about sports betting odds, prediction markets, win probabilities, market sentiment, or "who is favored to win" questions. Don't use when: user asks about actual match results, scores, or statistics — use football-data or fastf1 instead. Don't use for historical match data. Don't use for news — use sports-news instead. Don't confuse with Kalshi — Polymarket focuses on crypto-native prediction markets with deeper sports coverage; Kalshi is a US-regulated exchange with different market structure.
wnba-data
by machina-sports
WNBA data via ESPN public endpoints — scores, standings, rosters, schedules, game summaries, play-by-play, win probability, injuries, transactions, futures, team/player stats, leaders, and news. Zero config, no API keys. Use when: user asks about WNBA scores, standings, team rosters, schedules, game stats, box scores, play-by-play, injuries, transactions, betting futures, team/player statistics, or WNBA news. Don't use when: user asks about NBA (use nba-data), college basketball (use cbb-data), or other sports.
nhl-data
by machina-sports
NHL data via ESPN public endpoints — scores, standings, rosters, schedules, game summaries, play-by-play, injuries, transactions, futures, team/player stats, leaders, and news. Zero config, no API keys. Use when: user asks about NHL scores, standings, team rosters, schedules, game stats, box scores, play-by-play, injuries, transactions, betting futures, team/player statistics, or NHL news. Don't use when: user asks about other hockey leagues (AHL, KHL, college hockey), or other sports.