gosling-lang/gosling.js

Grammar of Scalable Linked Interactive Nucleotide Graphics

Language: TypeScript - Size: 105 MB - Last synced at: 23 minutes ago - Pushed at: 25 days ago - Stars: 177 - Forks: 30

vitessce/vitessce

Vitessce is a visual integration tool for exploration of spatial single-cell experiments.

Language: JavaScript - Size: 53.3 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 208 - Forks: 48

higlass/higlass

Fast, flexible and extensible genome browser.

Language: JavaScript - Size: 154 MB - Last synced at: 3 days ago - Pushed at: 5 days ago - Stars: 324 - Forks: 52

hms-dbmi/vizarr

A minimal Zarr image viewer based on Viv.

Language: TypeScript - Size: 39.2 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 150 - Forks: 22

hubmapconsortium/ingest-validation-tools

HuBMAP data submission guidelines, and tools which check that submissions adhere to those guidelines.

Language: Python - Size: 5.39 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 8 - Forks: 18

hms-dbmi/UpSetR

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

Language: R - Size: 30 MB - Last synced at: 2 days ago - Pushed at: 10 months ago - Stars: 794 - Forks: 160

hms-dbmi/viv

Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.

Language: JavaScript - Size: 14.9 MB - Last synced at: 5 days ago - Pushed at: 8 days ago - Stars: 310 - Forks: 49

hms-dbmi/gehlenborglab-website

Code for HIDIVE Lab website.

Language: TypeScript - Size: 258 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 9 - Forks: 38

hubmapconsortium/portal-ui

HuBMAP Data Portal front end

Language: TypeScript - Size: 31.3 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 13 - Forks: 2

vitessce/vitessce-python

Python API and Jupyter widget for Vitessce

Language: Python - Size: 34.9 MB - Last synced at: about 1 hour ago - Pushed at: 9 days ago - Stars: 45 - Forks: 8

hubmapconsortium/portal-visualization

Given HuBMAP Dataset JSON, creates a Vitessce configuration

Language: Python - Size: 312 KB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 1 - Forks: 1

hubmapconsortium/portal-containers

Docker containers to pre-process data for visualization in the portal

Language: Python - Size: 767 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 1

higlass/clodius

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

Language: Python - Size: 26.9 MB - Last synced at: about 11 hours ago - Pushed at: 22 days ago - Stars: 39 - Forks: 21

gosling-lang/gos

A declarative interactive genomics visualization library for Python.

Language: Python - Size: 13 MB - Last synced at: 13 days ago - Pushed at: 17 days ago - Stars: 225 - Forks: 14

gzuidhof/zarr.js

Javascript implementation of Zarr

Language: TypeScript - Size: 979 KB - Last synced at: about 15 hours ago - Pushed at: 12 months ago - Stars: 147 - Forks: 26

vitessce/vitessce-python-tutorial

Notebooks for HuBMAP tutorial session (January 2023)

Language: Jupyter Notebook - Size: 56.1 MB - Last synced at: about 2 months ago - Pushed at: almost 2 years ago - Stars: 7 - Forks: 1

gosling-lang/gosling-website

Documentation website of Gosling

Language: MDX - Size: 36.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 5

vitessce/vitessceR

R API and htmlwidget for Vitessce

Language: R - Size: 49 MB - Last synced at: about 2 months ago - Pushed at: 8 months ago - Stars: 40 - Forks: 9

parklab/nozzle

Nozzle is a report generation toolkit for data analysis pipelines implemented in R.

Language: R - Size: 1.47 MB - Last synced at: 20 days ago - Pushed at: about 9 years ago - Stars: 68 - Forks: 21

higlass/higlass-manage

A utility script to manage local docker instances of HiGlass

Language: Python - Size: 153 KB - Last synced at: 7 days ago - Pushed at: almost 2 years ago - Stars: 24 - Forks: 9

hms-dbmi/upset-altair-notebook

Jupyter Notebooks and other code for Altair-based Interactive UpSet Plots

Language: Jupyter Notebook - Size: 382 KB - Last synced at: 18 days ago - Pushed at: over 3 years ago - Stars: 31 - Forks: 4

gosling-lang/gos-example

Language: Jupyter Notebook - Size: 210 KB - Last synced at: 13 days ago - Pushed at: 6 months ago - Stars: 4 - Forks: 0

higlass/higlass-multivec

Multivec Tracks for Higlass

Language: HTML - Size: 3.3 MB - Last synced at: about 11 hours ago - Pushed at: 10 months ago - Stars: 7 - Forks: 6

higlass/higlass-docker

Builds a docker container wrapping higlass-server and higlass-client in nginx

Language: Shell - Size: 5.66 MB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 32 - Forks: 14

Caleydo/caleydo 📦

Caleydo - Visualization for Molecular Biology

Language: Java - Size: 1.39 GB - Last synced at: 5 months ago - Pushed at: over 8 years ago - Stars: 58 - Forks: 14

hubmapconsortium/tableschema-to-template

Given a Frictionless Table Schema, generate an Excel template with input validation

Language: Python - Size: 77.1 KB - Last synced at: 13 days ago - Pushed at: over 2 years ago - Stars: 12 - Forks: 3

higlass/higlass-server

Server component for HiGlass that manages and serves tiled data

Language: Python - Size: 125 MB - Last synced at: about 1 month ago - Pushed at: about 2 years ago - Stars: 19 - Forks: 21

covidclinical/website

Repository for covidclinical.net website.

Language: HTML - Size: 6.66 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 3

hubmapconsortium/hubmap-api-py-client

Python client for the Cells API

Language: Python - Size: 97.7 KB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

hms-dbmi/smart-fhir-drill

Test performance of FHIR API implementations. 🚒

Language: JavaScript - Size: 36.1 KB - Last synced at: about 1 year ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0

hms-dbmi/mHealthieR

R package to assess and evaluate longitudinal mHealth sensor data.

Language: R - Size: 86.9 KB - Last synced at: about 1 year ago - Pushed at: almost 8 years ago - Stars: 3 - Forks: 0

hms-dbmi/ome-tiff-tiler

Creates a Docker image that can create tiles from OME-TIFF files

Language: Python - Size: 25.4 KB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

hms-dbmi/map-explorer

Use MAP to explore EHR data for individual patients.

Language: R - Size: 2.13 MB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 0

hms-dbmi/list-aws-resources

Using AWS CLI, produce a TSV summarizing AWS resources in use.

Language: Shell - Size: 2.93 KB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 1

hms-dbmi/generate-static-site

Creates a basic Jekyll repo, S3 bucket, and limited priv user which Travis will use to push updates

Language: Shell - Size: 7.81 KB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

hms-dbmi/gehlenborg-lab-best-practices

Guidelines for creating medium-scale visualization software

Size: 4.88 KB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 0

hms-dbmi/c19i2b2-website

Website for c19i2b2 consortium project.

Language: CSS - Size: 822 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

hms-dbmi/cistrome-higlass-demo

HiGlass demo with Cistrome data sets.

Language: HTML - Size: 10.7 KB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

hms-dbmi/bmi713-visualization-lecture-2018

Language: HTML - Size: 36.7 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 2

hms-dbmi/hic-data-analysis-bootcamp

Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.

Language: Jupyter Notebook - Size: 291 MB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 185 - Forks: 46

hms-dbmi/3d-genome-processing-tutorial

A 3D genome data processing tutorial for ISMB/ECCB 2017

Language: Jupyter Notebook - Size: 188 MB - Last synced at: about 1 year ago - Pushed at: almost 8 years ago - Stars: 48 - Forks: 9

hms-dbmi/UpSetR-paper

Data and scripts for UpSetR paper.

Language: R - Size: 8.62 MB - Last synced at: about 1 year ago - Pushed at: about 8 years ago - Stars: 8 - Forks: 1

th789/vitessce-shiny

R Shiny app for Vitessce, an integrative and interactive data visualization tool for exploration of spatial single-cell experiments.

Language: R - Size: 27.9 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

hms-dbmi/cistrome-explorer

Interactive visual analytic tool for exploring epigenomics data w/ associated metadata, powered by HiGlass and Gosling

Language: Jupyter Notebook - Size: 44.1 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 0

vitessce/vitessce-data

Utils for loading HuBMAP data formats

Language: Python - Size: 3.94 MB - Last synced at: 13 days ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 4

hms-dbmi/UpSetR-shiny

A Shiny wrapper for the UpSetR R package (https://github.com/hms-dbmi/UpSetR).

Language: R - Size: 373 KB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 20 - Forks: 6

hms-dbmi/altair_examples

Juptyer Notebooks with Altair Examples

Language: Jupyter Notebook - Size: 48.8 KB - Last synced at: about 1 year ago - Pushed at: almost 7 years ago - Stars: 9 - Forks: 4

refinery-platform/refinery-platform

The Refinery Platform is a data management, analysis and visualization system for bioinformatics and computational biology applications. The platforms consists of three major components: a data repository with rich metadata capabilities, a workflow engine based on the popular Galaxy system, and visualization tools to support the exploration and interpretation of results at all stages of the analysis process.

Language: Python - Size: 124 MB - Last synced at: 9 months ago - Pushed at: over 2 years ago - Stars: 102 - Forks: 24

hms-dbmi/halyos

Redesigning the Patient Portal Experience with SMART on FHIR.

Language: JavaScript - Size: 4.38 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 22 - Forks: 5

hubmapconsortium-graveyard/directory-schema 📦

Use JSON Schema to validate directory structures

Language: Python - Size: 11.7 KB - Last synced at: 1 day ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 1

higlass/higlass-website 📦

HiGlass Project Website

Language: HTML - Size: 12.7 MB - Last synced at: about 1 year ago - Pushed at: about 6 years ago - Stars: 3 - Forks: 4

hubmapconsortium-graveyard/img2zarr 📦

Python utility for converting images to zarr chunked arrays

Language: Python - Size: 20.5 KB - Last synced at: 11 days ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

hubmapconsortium-graveyard/search-schema 📦

JSON Schema for documents in HuBMAP Elasticsearch

Language: Python - Size: 60.5 KB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 1

covidclinical/visualization-notebooks

Jupyter Notebooks and other code for 4CE data visualizations.

Language: Jupyter Notebook - Size: 20.1 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 10 - Forks: 4

hubmapconsortium-graveyard/portal-images 📦

Images for portal-ui

Size: 12.8 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

hubmapconsortium-graveyard/portal-style-guide 📦

Style guide for HuBMAP Portal development.

Language: JavaScript - Size: 6.2 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

hubmapconsortium/portal-docs 📦

Markdown documentation to be displayed in the Portal

Size: 464 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 5

hubmapconsortium/hubmap-api-js-client 📦

Javascript client for the Cells API

Language: JavaScript - Size: 256 KB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

Caleydo/vistories_website

Vistories Website

Language: HTML - Size: 137 MB - Last synced at: 5 months ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

hms-dbmi/OncoThreads

OncoThreads longitudinal cancer genomics visualization project.

Language: JavaScript - Size: 21.8 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 1

hms-dbmi/genocat

Genomic Visualization Catalog

Language: HTML - Size: 185 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 12 - Forks: 7

gosling-lang/gosling-theme

Styling themes for Gosling.js

Language: TypeScript - Size: 431 KB - Last synced at: about 7 hours ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 2

hms-dbmi/connections.careers

Website for a video project that documents the training experiences of predoctoral and postdoctoral trainees from 16 National Library of Medicine-funded biomedical informatics and data science training programs.

Language: JavaScript - Size: 20.6 MB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

hms-dbmi/viv-tile-benchmark

A benchmark to compare data retrieval performance for OME-TIFF and Zarr using different tile sizes and HTTP protocol versions.

Language: JavaScript - Size: 113 KB - Last synced at: 13 days ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

Caleydo/stratomex_js

StratomeX for the visual exploration of genomic stratification of diseases @JKU-ICG

Language: TypeScript - Size: 255 KB - Last synced at: 5 months ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 2

hms-dbmi/shinyVCT

Visual Consent Tool Shiny app.

Language: R - Size: 2.35 MB - Last synced at: about 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 2

refinery-platform/visualization-tools

Registry for Visualization Tool Annotations that are compatible with Refinery (https://github.com/refinery-platform/refinery-platform)

Language: Python - Size: 115 KB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 1

hms-dbmi/decart-2019-data-visualization

Materials for the DeCART 2019 Summer School Data Visualization Course

Language: Jupyter Notebook - Size: 61.5 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 3 - Forks: 14

hms-dbmi/higlass-story

A tool to create scrollytelling-based stories with HiGlass.

Language: JavaScript - Size: 1.64 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

refinery-platform/clodius-galaxy

Galaxy tool wrapper around Clodius: https://github.com/hms-dbmi/clodius

Size: 292 KB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

ngehlenborg/scifigure Fork of prpatil/scifigure

R package for generating a reproducibility/replicability study comparison visualization

Language: R - Size: 1.11 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

ngehlenborg/scifigure-utils

Utilities for the scifigure package.

Language: R - Size: 65.4 KB - Last synced at: about 1 month ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0