How do I install the Window Maker skill?

Run npx skillmds add vimalinx/window-maker in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Window Maker safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: docs only. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Window Maker?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Window Maker free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Window Maker?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Window Maker by vimalinx — Agent Skill

Name: Window Maker
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

File contents

window-maker

Quick Start

Command: windowMaker [-g genome.txt | -b intervals.bed] [-w size | -n count] [options]
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/windowMaker
Full reference: See references/help.md

When To Use This Tool

Tile a genome or interval set into fixed-width windows.
Create sliding windows by combining -w with -s.
Split each source interval into a fixed number of windows with -n.
Add window identifiers for downstream joins, coverage summaries, or matrix construction.

Common Patterns

# 1) Make non-overlapping 1 Mb genome windows
windowMaker \
  -g genome.txt \
  -w 1000000

# 2) Make sliding 10 kb windows with 5 kb step
windowMaker \
  -g genome.txt \
  -w 10000 \
  -s 5000

# 3) Split each BED interval into 20 windows and label by window number
windowMaker \
  -b regions.bed \
  -n 20 \
  -i winnum

Recommended Workflow

Choose the source domain first: whole-genome tiling with -g or per-interval tiling with -b.
Choose fixed width (-w) versus fixed count (-n) based on the downstream statistical design.
Add -s only when you intentionally want overlapping sliding windows.
Use -i and optionally -reverse when downstream tools need stable window IDs rather than anonymous coordinates.

Guardrails

You must provide one interval source: -g or -b.
You must provide one windowing mode: -w or -n.
-s is meaningful with -w window-size mode, not as a replacement for -n.
The genome file is tab-delimited chromosome name plus size; a FASTA .fai works because bedtools reads only the first two columns.
Prefer -h for help; GNU-style --version on this wrapper emits errors before exiting.

---name: window-makerdescription: Use when you need to create adjacent or sliding windows across a genome or BED file for binning genomic regions into fixed-size or fixed-count intervals.--- # window-maker ## Quick Start - **Command:** `windowMaker [-g genome.txt | -b intervals.bed] [-w size | -n count] [options]` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/windowMaker` - **Full reference:** See `references/help.md` ## When To Use This Tool - Tile a genome or interval set into fixed-width windows. - Create sliding windows by combining `-w` with `-s`. - Split each source interval into a fixed number of windows with `-n`. - Add window identifiers for downstream joins, coverage summaries, or matrix construction. ## Common Patterns ```bash # 1) Make non-overlapping 1 Mb genome windows windowMaker \ -g genome.txt \ -w 1000000 ``` ```bash # 2) Make sliding 10 kb windows with 5 kb step windowMaker \ -g genome.txt \ -w 10000 \ -s 5000 ``` ```bash # 3) Split each BED interval into 20 windows and label by window number windowMaker \ -b regions.bed \ -n 20 \ -i winnum ``` ## Recommended Workflow 1. Choose the source domain first: whole-genome tiling with `-g` or per-interval tiling with `-b`. 2. Choose fixed width (`-w`) versus fixed count (`-n`) based on the downstream statistical design. 3. Add `-s` only when you intentionally want overlapping sliding windows. 4. Use `-i` and optionally `-reverse` when downstream tools need stable window IDs rather than anonymous coordinates. ## Guardrails - You must provide one interval source: `-g` or `-b`. - You must provide one windowing mode: `-w` or `-n`. - `-s` is meaningful with `-w` window-size mode, not as a replacement for `-n`. - The genome file is tab-delimited chromosome name plus size; a FASTA `.fai` works because bedtools reads only the first two columns. - Prefer `-h` for help; GNU-style `--version` on this wrapper emits errors before exiting.

Frequently asked questions