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higlass

15 indexed repositories · View on GitHub

higlass
Fast, flexible and extensible genome browser.

JavaScript · 342 stars
higlass-python
Python bindings to and Jupyter Notebook+Lab integration for the HiGlass viewer

Python · 66 stars
clodius
Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.

Python · 39 stars
simple-httpfs

Python · 37 stars
higlass-docker
Builds a docker container wrapping higlass-server and higlass-client in nginx

Shell · 34 stars
higlass-manage
A utility script to manage local docker instances of HiGlass

Python · 24 stars
higlass-server
Server component for HiGlass that manages and serves tiled data

Python · 22 stars
negspy
Python NGS Repository

Python · 9 stars
higlass-app
A fully featured application around HiGlass for viewing, exploring, and annotating 1D and 2D genomic data

JavaScript · 8 stars
higlass-multivec
Multivec Tracks for Higlass

JavaScript · 8 stars
gene_annotations

Python · 6 stars
higlass-sequence
Nucleotide sequence track for HiGlass

JavaScript · 6 stars
higlass-transcripts
Gene transcripts track for HiGlass

JavaScript · 6 stars
higlass-gnomad
Display gnomAD data in HiGlass

JavaScript · 2 stars
higlass-linear-labels-track

JavaScript · 1 star

Open All

https://github.com/pkerpedjiev/million-primes is 👎 Open

higlass/higlass-linear-labels-track#1 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Parameterize # of cores Open

higlass/higlass-docker#3 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Redundant uninstall-reinstalls Open

higlass/higlass-docker#8 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Choose s3-fs-thing and implement Open

higlass/higlass-docker#19 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Load test EC2 Open

higlass/higlass-docker#29 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Create AWS user for use by Docker instance Open

higlass/higlass-docker#30 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
script for bucket creation and priv setting Open

higlass/higlass-docker#31 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Why are nginx logs going to /tmp? Open

higlass/higlass-docker#36 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Test that redis is actually doing something Open

higlass/higlass-docker#42 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Consider separating nginx and running it in its own container Open

higlass/higlass-docker#43 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Shouldn't COPY still use cache? Open

higlass/higlass-docker#45 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Redeploy preserves data / continuous deployment / zero downtime? Open

higlass/higlass-docker#47 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Could we link to the google doc describing provisioning? Open

question

higlass/higlass-docker#55 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Hitting /tiles in a test should exercise Redis Open

higlass/higlass-docker#68 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
New server, think I've ingested data, but console errors Open

higlass/higlass-docker#102 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Speed up performance of local server Open

enhancement

higlass/higlass-docker#116 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Unable to generate view configs on locally deployed HiGlass Open

bug

higlass/higlass-docker#133 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
Replace series / Hit "escape" / Data is gone Open

higlass/higlass-docker#135 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 17, 2026
What should be the expected behavior for truncated files? Open

higlass/higlass-docker#136 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Implicit ingest? Open

question

higlass/higlass-docker#137 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Minimize number of RUNS in Dockerfile Open

higlass/higlass-docker#141 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Host hglib.js on the docker container so that it doesn't get pulled from unpkg.org Open

higlass/higlass-docker#142 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Change list of pre-installed tracks/datasets Open

higlass/higlass-docker#144 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
consider allowing custom ip subnet in docker network create Open

higlass/higlass-docker#148 · 1 comment · 1 reaction · 0 assignees · Indexed Sep 17, 2026
images do not work out of the box (v0.5.0-rc7 and v0.4.17) Open

higlass/higlass-docker#151 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
local docker error Open

higlass/higlass-docker#152 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Problem with search gene for mm9 in Genome Position Search Box Open

higlass/higlass-docker#153 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Use un-privileged port in Dockerfile Open

higlass/higlass-docker#154 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Export view as XXX: not working Open

higlass/higlass-docker#155 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Error retrieving tilesetInfo from: /api/v1 Open

higlass/higlass-docker#159 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Can't search annotation by gene name Open

higlass/higlass-docker#161 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Building the container Open

higlass/higlass-docker#165 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
higlass-manage start raises error ValueError: invalid literal for int() with base 16: b'' Open

higlass/higlass-docker#169 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Can not load and view the mcool file Open

higlass/higlass-docker#173 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Zoom in view is blurry in top panel but clear in middle pannel? Open

higlass/higlass-docker#174 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Docker higlass-container fails to start if userns-remap is in use Open

higlass/higlass-docker#175 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Vulnerable nginx Open

higlass/higlass-docker#176 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
how to add plugin tracks into docker? Open

higlass/higlass-docker#177 · 11 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
How to find out the site_url to access a local docker desktop container remotely? Open

higlass/higlass-docker#179 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
higlass-server/manage.py ingest_tileset doesn't work Open

higlass/higlass-docker#180 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Cannot view .cool file Open

higlass/higlass-docker#181 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
superuser as admin - design for better authorization model Open

higlass/higlass-docker#182 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
security (CVEs) issues - 4 critical and 11 high - most fixed by upgrading components Open

higlass/higlass-docker#183 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Add to the github actions to do a security scan of the higlass-docker container Open

higlass/higlass-docker#184 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Custom colormap in top/bottom HiC maps Open

higlass/higlass-docker#185 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
provide a kubernetes configuration for HiGlass components vs single docker container Open

higlass/higlass-docker#186 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
nginx ReverseProxy/Subpath possible? Open

higlass/higlass-docker#187 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026
NA Open

higlass/higlass-docker#189 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
saving and loading a session via config file? Open

higlass/higlass-docker#190 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 17, 2026
Can't pull higlass/higlass-docker Open

higlass/higlass-docker#191 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 17, 2026

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