What chromosomix is

chromosomix shows contact maps, genome tracks and 3D models side by side, straight from your files. It runs in your web browser — at https://chromosomix.app/, as a desktop app or as one HTML file — and uploads nothing. A chromosomix command line runs the same analyses in a script.

What you can do with it

• Read a contact map at every resolution it stores: raw, balanced, observed over expected or as a correlation (Reading a contact map).
• Line tracks up with it — bigWig, peaks, genes, BAM — on any edge of the map, or in a genome browser of their own.
• Compare maps: two in one square, their ratio (Comparing two maps), or several side by side.
• See a 3D model beside the map, each pointing at the other (3D models beside the map).
• Run analyses in the page — P(s), insulation, compartments, loops, APA, virtual 4C and more — each checked against the package it reproduces (Analyses).
• Repeat them in a shell: every run is written to the console as the command that repeats it (From the app to a script).
• Keep and share the work as a PDF or PNG (Figures and export), a link or a workspace file (Sessions, workspaces and links).

What it reads

What	Formats
Contact maps	.cool, .mcool, .hic, .scool, HiC-Pro, .pairs
Tracks and features	bigWig, bedGraph, bigBed, BED, narrowPeak, GTF, GFF3, VCF, BAM and more
Interactions	BEDPE, interact, bigInteract, longrange
Sequences	FASTA, .2bit, chrom.sizes
3D models	g3d, .3dg, bed3d, PDB

From your disk, any web host that serves byte ranges, Dropbox, Google Drive, a private bucket, a UCSC track hub, or the data stores the app offers: Opening files. Every format is in Files, hosts and stores.

Why it is built this way

• No server, no account. Reading, drawing and every analysis happen in your browser.
• Nothing is uploaded. A file on your disk is read in place; unpublished data never leaves your machine.
• Remote files are read by range: one chromosome of a large .mcool costs a few requests, not a download.
• It works offline after one visit, and the map stays live while a task runs.

What the browser keeps is listed in the command palette under What this browser is remembering (Privacy).

Where next

• Ways to use it: the web app, the desktop app, one file, a notebook or a shell.
• Your first map: open a public map, step by step.
• A tour of the window: what each part of the screen is for.

chromosomix is free software (GPL-3.0 or later), at https://github.com/js2264/chromosomix (Source code and contributing).