Glossary

The words you meet on screen and in these pages. Where a page explains one at length, its entry links there.

Aggregate peak analysis (APA)

The map averaged around a set of loops or features, against a control, to show whether they are enriched as a group. See Aggregate peak analysis.

Allow access

The button a tab shows when Chrome or Edge remembers a local file but needs your permission to read it again, after a restart say; one press allows them all. See Sessions, workspaces and links.

Arms, origin and terminus

A bacterial chromosome’s replication origin, set in the Chromosomes table or by the Origin and terminus task, splits it into two arms that meet at the terminus. See Origin and terminus and Inter-arm alignment.

Assembly

A genome’s sequences and their lengths, read from a FASTA, a .2bit, a chrom.sizes, a cytoBand, a map, or the header of a bigWig, bigBed or BAM. See Reference sequences.

Balancing

Correcting a map for how visible each bin is (its total contacts), so its rows and columns compare. balanced reads the file’s own weights; VC, square-root VC and ICE are computed in the page. balance=true in a link. See Reading a contact map.

Batch

The box above the Tracks card’s list when two rows or more are ticked: its settings apply to all of them, and read mixed where they differ. See Annotations and bookmarks.

Bin

A fixed stretch of sequence, one row or column of a map. A map’s resolution is its bin size.

Bookmark

A saved place, with the resolution it was found at, on the Bookmarks card. See Annotations and bookmarks.

Bucket

An object store, such as Amazon S3, Cloudflare R2 or Google Cloud Storage, serving files by byte range. connect a bucket… connects a prefix as a folder, with a key if it is private. See Hosting your data.

Called set

What a task found — boundaries, domains, peaks, A/B segments, sites, loops — as one row of the Tracks card, drawn beside the map or over it. See How analyses run.

Card

A titled box in a side panel, such as Tracks or Map. Drag it by its heading to another panel; Put every card back in its own panel, in the command palette, undoes that. See A tour of the window.

Cell

One place in a deck: a map, a structure cell (a 3D model), a tracks cell (the tab’s tracks alone), or an empty cell, which takes a map, a track or a structure dropped on it. See Maps side by side.

Circular sequence

A sequence whose ends join, such as a plasmid, ticked in the Chromosomes table’s circular column; a file’s first opening ticks those that look circular. Windows may cross the join, and most tasks measure distance the short way round.

Command palette

Ctrl+P (⌘+P on a Mac): every command by name, with its key. ? lists the keys. See Keyboard and command palette.

Comparison

A second map in the lower-left triangle of the same square, on one colour scale, or the two maps’ ratio or difference. Both need the same bin size and sequences; otherwise use a deck. See Comparing two maps.

Compartments

The checkerboard of a Hi-C map: chromatin of two kinds, A and B, each in contact with its own. The Compartments task finds them as E1, its sign phased by genes, a track or GC content. See Compartments.

Connected folder

A folder on your computer, a bucket prefix, a Google Drive folder or your Dropbox, listed in the Files panel. In a browser tab a folder on your computer lasts the visit (this visit); an installed app keeps it. See Opening files.

Console

What the window has done, as the chromosomix commands that repeat it. Ctrl+`, the key left of 1, opens it; this browser keeps a week of it, 500 lines at most. See The console.

Contacts box

The contacts box over the map draws every map in the tab at the number of contacts you type, subsampled exactly if it has more and oversampled with Boost-HiC if fewer, to compare depths. contacts= in a link. See Comparing two maps.

Coordinates

What you read and type is 1-based and inclusive, as in IGV and UCSC, and the command line takes the same: IV:1,000,001-1,400,000. A map’s region in a link is cooler’s 0-based, half-open IV:1000000-1400000. See Link keys.

Deck

Cells side by side in one tab, panned and zoomed together, opened by the + down the map’s right edge or along its bottom. Its maps need share only coordinates. maps= in a link. See Maps side by side.

Desktop app

chromosomix for macOS and Linux, from the releases page: the same viewer on your disk, which can also read a compressing host by range. See Web, desktop or one file.

Detached

A track from a local file after a reload: its settings are back but not its bytes, so its row offers to read the file again. A computed track offers recompute instead. See Sessions, workspaces and links.

Domain

A square along the diagonal, often called a TAD: a stretch in more contact with itself than with its neighbours. Insulation and the directionality index find its borders; TAD annotation finds the domains, nested where they nest. See TAD annotation.

Edge

The side of a map a track’s lane is on: top, right, bottom or left. A file dropped on the middle of a map is that map’s alone. See Annotations and bookmarks.

Embed

The viewer in another web page, as an <iframe> with ?embed=1: one view of one file, with no header or tabs. See Embedding in a web page.

Eye, × and grip

On each row of the Contact maps, Tracks and Structures cards, the eye shows or hides, the × lets go, and the grip drags the row along the card, onto a cell or onto a + edge. See Maps side by side.

Facet

One of a store’s columns, down the side of its page, with every value counted. Ticks in one facet add up; ticks in two narrow each other. See Data stores.

Feature set

A track of intervals — peaks, genes, any BED — that a task can take as its features. The star on its Tracks row makes it the set the feature search and the tasks read by default. See Tracks and features.

Framing and provenance

The framing is what a task runs on — the window, bin size, score and the rest — taken when you press run, so the result stands when you pan away. The provenance adds the task, its parameters, the file, the build and the time, and goes into every export that can hold it. See How analyses run.

Genome browser

The 1D view: tracks along a sequence, with or without a map. A track or a reference opened on its own starts one. view=browser in a link. See The genome browser.

Group

Tracks sharing one value axis, in a lane each or overlaid, so two strands of an experiment share a ceiling; set to each, every member keeps its own. On the Groups card. See Annotations and bookmarks.

Ideogram

A chromosome drawn from a UCSC cytoBand file, with its bands. A band’s name, such as Xq28, works in the locus box. See Tracks and features.

Insulation

How much contact crosses each bin, in a diamond-shaped window slid along the diagonal. Its dips are domain boundaries, higher in the hierarchy as the window widens. The task Diamond insulation. See Diamond insulation.

Lane

One placement of a track, on one map and one edge; a track can have several, or none. See Annotations and bookmarks.

Lead and companion

In a deck, the lead (the first map, in the app) is the tab’s own file, which names the tab and holds its tables, tracks and comparison; the companions are the maps beside it. See Maps side by side.

Level

What one row and column of the map stand for: a bin, or a whole sequence summed into one cell. level=contig in a link. See Reading a contact map.

Lock and chain

What moves a deck’s maps together. The lock follows places in base pairs, across resolutions; a map’s chain says whether it follows. See Maps side by side.

Locus

A window in the genome browser, 1-based and inclusive: chrI:1,001-20,000. The locus box also finds a gene or a band by name. See Moving around.

Loop

A dot off the diagonal: two places in more contact than their distance predicts. Loop calling and Pattern detection (Chromosight) find them. See Loop calling.

Mark

A line, an arrowhead or a rectangle you draw on the map, typed as coordinates or picked, on the Manual annotations card. Marks leave as BED and BEDPE files. See Annotations and bookmarks.

Metadata annotation

A column the file carries about its sequences or bins, such as a balancing weight, drawn like a track. On the Metadata annotations card. See Annotations and bookmarks.

O/E

Observed over expected: each cell divided by what its distance from the diagonal predicts, leaving what is unusual. A switch beside the score, not a score. oe=true in a link. See Reading a contact map.

P(s)

Contact probability against genomic separation s: the fall of contact with distance that every Hi-C map shares, and the expected O/E divides by. The task Contact probability P(s). See Contact probability P(s).

Panel

A column either side of the map: General, Annotations, Aesthetics and Analysis, with Files while a folder is connected. See A tour of the window.

Pinned release

A release kept for good at https://chromosomix.app/v/<tag>/, which takes the same links and embeds as the root and goes on drawing the same picture. About lists the published builds. See Running your own copy.

Refine on zoom

A preference in the command palette, off by default: zooming past what was read reads the window again at a finer resolution, rather than magnifying it. See Moving around.

Resolution

A map’s bin size, such as 5 kb. An .mcool or a .hic stores several, named in an address by ::/resolutions/<bin size>; one summed from whole bins of a stored one is marked *: 3 kb*. See Contact maps.

Score

What a map’s cells hold: raw or balanced counts, VC, square-root VC or ICE, the expected count, the correlation compartments are read from, or another column of the file. score= in a link. See Reading a contact map.

Sequence

One chromosome, contig or plasmid. The app says sequence, and chromosome or contig where it reports a file’s own word, as in the Chromosomes table. See Moving around.

Session

What a tab holds — a file, its views, tracks, marks and settings — called a tab on screen; also such a tab written down, as a store’s pre-configured session or an example under Pick an example session. See Sessions, workspaces and links.

Share link

A link to one tab from Share this tab as a link, holding the tab after the #, which no server sees. shorten with is.gd shortens it through that service. See Sessions, workspaces and links.

Single file

The whole viewer as one HTML file, chromosomix-<tag>.html, on every release. It opens from a disk with no network, and reads local files only. See Web, desktop or one file.

Splice junction

An intron reads were seen to skip, and how many — from STAR’s SJ.out.tab, a junctions BED, leafcutter’s .junc or a spliced BAM — drawn as a sashimi arc as tall as its count. See Tracks and features.

Star

Which map of a deck the Analysis panel reads, the Map card sets and the File card describes. With none starred (press the filled star), the Map card sets every map and the tasks that read a map wait. See Maps side by side.

Status bar

The strip at the foot of the window. Its read gives the requests and bytes this tab’s files have cost. See A tour of the window.

Store

A catalogue of published files, browsed in the store drawer: one JSON file, or a UCSC track hub. Built in: RSG lab data, IGV genomes, 4DN open data, ENCODE, DNA Zoo and Roadmap; Add a custom store opens others. See Data stores and Your own data store.

Store drawer

The panel down the left where a store is browsed, opened by a store’s tile on the landing page, the header’s toggle or \. One serves every tab. See Data stores.

Structure and model

A structure is a 3D file of beads (g3d, .3dg, bed3d or PDB) drawn in a structure cell; a model is one set of its coordinates, a chain one sequence’s beads, a bead one row. Model from the map makes one from the contacts. See 3D models beside the map.

Synthetic track

A task’s result, or the ratio or difference of two tracks, as a row of the Tracks card marked *. After a reload its row offers recompute. See How analyses run.

Tab

One session, in the strip under the header: a file and what you did with it, twelve at most. o opens one, Ctrl+< and Ctrl+> step between them, and F2 or a double-click renames one. See A tour of the window.

Task

One analysis on the Analysis panel, under 2D tasks, 3D tasks or 1D tasks. Pressed, it opens in the Analysis drawer while the map stays live; a greyed task says what to load first. See How analyses run.

Track

A 1D dataset you loaded — a bigWig, a BED, gene models, reads — on the Tracks card, drawn in one or more lanes. See Tracks and features.

Track hub

UCSC’s format for publishing tracks: a hub.txt naming a genomes.txt, which names a trackDb.txt for each assembly. Connect to a UCSC hub reads one as a store. See UCSC track hubs.

Transform and colour scale

The transform (log1p, log10, log2 or none) is the scale a value is coloured on, clipped at vmin and vmax, automatic unless you set them. The colour map is the ramp; RdBu_r, BuWtRd and seismic are diverging, for a ratio or an O/E. See Reading a contact map.

Turn (the 45° view)

One sequence’s map rotated 45°, with distance from the diagonal up the side; it turns every map of the deck. flip=true in a link. See The 45° view.

Tutorial

A first session played on the live window, step by step, on 4DN’s Hi-C of K562. Start it under New here? on the landing page, in About, or with Guided tutorial in the command palette. See The guided tutorial.

View

What a tab shows of its file: the Chromosomes table, the whole genome, a region, some sequences, the genome browser, or an .scool’s cells. view= in a link. See Link keys.

Virtual 4C

An anchor’s contacts with everything around it, as a track; the task 4C profile from an anchor. See 4C profile from an anchor.

Window

The browser tab or desktop app window chromosomix runs in. The theme and each panel’s width and fold belong to it, whatever tab is in front. See A tour of the window.

Workspace

Every open tab in one .chromosomix.json, from Save every tab as a file (Ctrl+S, ⌘+S on a Mac). Dropped on the window, its tabs open beside yours; published, it opens from ?config=<address> or a store’s row. restore offers your last one back. See Sessions, workspaces and links.