Replacement for Epiviz

[adkinsrs]

This is going to be a place to list potential alternative tools to replace Epiviz as the epigenome browser/viewer for gEAR. Will include information such as list of options/features and datatypes/displays the candidate supports.

[adkinsrs]

IGV

https://igv.org/
https://igv.org/app/ (demo)
https://academic.oup.com/bioinformatics/article/39/1/btac830/6958554?login=false (paper)

I would imagine that we could use IGV.js depending on the memory requirements of viewing various tracks.

FEATURES

• Single JS file with no external dependencies
• JS-level API control for loading tracks, genomes, regions of interest, etc
• When creating the IGV browser, can set the initial state via JSON
  • Configuration options -> https://igv.org/doc/igvjs/#Browser-Creation/#browser-configuration-options
• Can create multiple browsers in an instance
• Has a number of hosted reference genomes, including all currently used in gEAR. There are methods for loading other genomes though
• Many JSON config entities can load from remote URL, so we do not have to keep everything on the VM
• Loadable sample information files can be made to sort, group, color, and filter samples
• Support for event handlers on track modification
• OAuth support for files behind a secure endpoint (not applicable in gEAR for now)

TRACKS

Track Type	Description	Associated File Formats
annotation	Non-quantitative genome annotations such as genes. This is the most generic track type.	bed, gff, gff3, gtf, bedpe, and others
wig	Quantitative genomic data, such as ChIP peaks and alignment coverage.	wig, bigWig, bedGraph
alignment	Sequencing alignments.	bam, cram
variant	Genomic variants	vcf
seg	Segmented copy number data.	seg
mut	Mutation data, primarily from cancer studies.	maf, mut
interact	Arcs representing associations or interactions between 2 genomic loci.	bedpe, interact, bigInteract
gwas	Genome wide association data (manhattan plots)	gwas, bed
arc	RNA secondary structure	bp, bed
junction	RNA splice junctions	bed
qtl	Quantitative trait locus	qtl
pytor	Copy number analysis	pytor, vcf
merged	Overlayed wig tracks

-- more content here --

[adkinsrs]

WashU Epigenome Browser

https://epgg.github.io/
https://epigenomegateway.wustl.edu/browser/ (demo)
https://academic.oup.com/nar/article/50/W1/W774/6567479 (this is 2022 paper - Don't think a 2025 paper is out yet)

FEATURES

• File-based and API-based JSON tracks
• Can use browser as a module in your web application
  • Not sure if it's possible to have multiple instances on a page, which would disqualify it if not
• I think the UI looks a bit more sleek
• Lots of existing tracks built in. Can use a table to filter and choose the ones you want.
• Remote track support. Just list filetype and URL
• Plot visualization support via App view
• Share options include emails, permalinks, QR codes, and embeds
• Multiple session support

TRACKS

Track Type	Description	Associated File Formats
annotation	Non-quantitative genome annotations such as genes. This is the most generic track type.	bed, bigbed, refbed, rgbpeak, bedcolor
numerical	Quantitative genomic data, such as ChIP peaks and alignment coverage.	bigWig, bedGraph
dynamic sequence	same track type as bigWig but each nucleotide is scored based on machine learning models	dynseq
alignment	Sequencing alignments.	bam
variant	Genomic variants	vcf
methylation	read depth, methylation context, and methylation level	methylc
categorical	bed file with a 4th categorical column	categorical
chromatin	Long range chromatin interaction	HiC, longrange, bigInteract
qbed	Discrete genomic data (i.e. transposon insertions)	qbed
genome-align	Pairwise genomic alignment	genomealign
Matplot	Multiple numerical tracks on the same X and Y axes to easily compare datasets
cool	Genomically-labeled sparse 2D arrays (cooler file)	API call
snp		API call

-- more content here --

[adkinsrs]

Gosling

https://gosling-lang.org/docs/
https://gosling.js.org/ (demo)
https://ieeexplore.ieee.org/document/9557192 (paper)

Also available as a Python package too - https://gosling-lang.github.io/gos/
For that we would return the HTML and embed in an iframe

v1.0.0 just released January 2025
Developed by a group at Harvard

FEATURES

• Formalized set of grammar and rules for genomic data visualizations
• Has a DummyTrack that can be used as a placeholder for non-Gosling visualizations
• Support for circular tracks
• Can overlay layouts or make them horizontal or vertical, as part of the grammar spec
• Tracks can have different "marks" such as point, line, text, and other advanced types to aide in visualization and representation of data
• Supports pre-aggregated tiled datasets through a HiGlass server
• Can link tracks and views for paired UI interaction (panning, zooming, etc)
• Support for semantic zooming, where different visual representations can be changed by zooming in or out
• Visualizations are responsive to screen size

TRACKS

• CSV
  • Support for tsv, csv, BED, BEDPE, and GFF and other small tabular data files
• GFF3
• VCF
  • Must have index file
• JSON
  • Adheres to Gosling's JSON spec
• BigWig
• BAM
• BED
• Vector (HiGlass Server)
  • One-dimensional quantitative values along genomic position
• MultiVec (HiGlass Server)
  • Two-dimensional quantitative values, one axis for genomic coordinate and the other for different samples
• BEDDB (HiGlass Server)

-- more content here --

[adkinsrs]

Found this site https://cmdcolin.github.io/awesome-genome-visualization/

[adkinsrs]

Figeno

https://github.com/CompEpigen/figeno
https://figeno.readthedocs.io/en/latest/index.html
https://academic.oup.com/bioinformatics/article/40/6/btae354/7690745 (paper)

Python-based

FEATURES

• Focus on multi-region views across genomic breakpoints and on long/split reads with base modification
• JSON configuration files
• Each track has "style" options (i.e. chr_axis has "default", "arrow", or "ideogram" options)
• Can export to SVG
• Multi-region views can show interactions across regions (i.e. HiC tracks)
• Horizontal and circular layout support
• Supports a symmetrical layout where regions are aligned on two rows, but the order of the tracks in the top row is reversed
  • Useful for structural variation tracks
• Not interactive (uses matplotlib) and requires a Flask server to operate

TRACKS

• chr_axis (genomic coordinates)
• genes (annotated genes)
• BED
• BigWig
• coverage
• HiC (.cool files - chromatin confirmation)
• alignments
• basemod_freq (haplotype-aware base modification frequency)
• copynumber
• sv (structural variants)
• ase (allele specific expression)

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[adkinsrs]

https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/40/6/10.1093_bioinformatics_btae354/1/btae354_supplementary_data.pdf?Expires=1746142735&Signature=AWedJerpUaDanQ1aOmnOx3gh3ZKDlTV23U7zT7OUdFmj6xdNsJ3HXBFEOLCsEIfzkOqlVD07ELEKIAp5p~WdZoK3JCTrT2GFKAveXmUpSaPgGsjQs71IzRCcYsY4uCZfNm0mvxbNjfN0ja0OHlCFLBkZEOmrPbmRLOQ1AwAidKKFkzE0wN2X3c385MUNMVagnJOSvi~ZQfJrW1jrs15iegjZcdJsg5EoMU5R3H~cQEfqXVKruh8oVsFdED5TH2egpC7u0UqOIg3N0clV1kOjOPhrjfKqOasjmUMBZAIZSuqa22oMKr3dbIkkwcMOw9qnIwlR7aQm-HccvULhSlF2Sg__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA

Useful comparison figure of Figeno to other genomic visualization tools

[adkinsrs]

Since I've only recently discovered the HiC plots, I thought it would be good include some information about those plots and what they are.

https://pmc.ncbi.nlm.nih.gov/articles/PMC7895846/

• Topologically associating domains (TADs) are fundamental units of three-dimensional (3D) nuclear organization. TADs are megabase-scale genomic regions that self-interact but rarely contact regions outside the domain
• TADs are identified based on regions of enriched contact density in Hi-C maps
  • This can also be broken down into hierarchical layers of organization
• The intensity within the HiC plot is essentially a pairwise interaction between two sets of coordinates within the region
• Generally 2 paired-end SAM alignment files can be used to construct an HiC matrix (as .h5 or potentially in .cool format which is also h5) and this matrix can be used to determine TADs
  • https://hicexplorer.readthedocs.io/en/latest/content/tools/hicBuildMatrix.html
  • https://hicexplorer.readthedocs.io/en/latest/content/tools/hicFindTADs.html

[adkinsrs]

We discussed looking at PeCan in ticket #704.

There is also the idea of getting a free academic license for the UCSC Genome Browser, but I think setup and embedding in a gEAR display may be difficult compared to the above tools. It would be much easier to build a link out to the remote UCSC Genome Browser but I am not sure that is wanted.

Link to slides for presentation
https://docs.google.com/presentation/d/1gQb0xX4kqEZdYbqt4Z0tkbSZdD8HuVPpLp3TCwypQvY/edit?usp=sharing