Discover GMOD/jbrowse-jupyter Open Source project

Source code for JBrowse 2, a modern React-based genome browser

457

jbrowse-components

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.

178

Apollo

Groovy

122

GBrowse

the Generic Genome Browser

R interface to the JBrowse 2 Linear Genome View.

Chado

the GMOD database schema

PLpgSQL

JBrowseR

vcf-js

High performance Variant Call Format (VCF) parser in pure JavaScript

Read CRAM v3 and v2 in node or in the browser

cram-js

Parse BAM and BAM index files in javascript for node and the browser

bam-js

JBrowse 1.x Plugin Registry

jbrowse-registry

HTML

dash_jbrowse

A suite of Dash components for JBrowse's embeddable components

Python

tabix-js

Read Tabix-indexed files, either with .tbi or .csi indexes, in node or the browser

Read FASTA files indexed with .fai indexes. Also supports BGZIP+.gzi

indexedfasta-js

parse and format streams of GFF3, for node or webpack

gff-js

GBrowse-Adaptors

Generate GD images of biological sequences and annotations

Bio-Graphics

A multiple sequence alignment viewer

react-msaview

Nodejs filehandle for reading bgzip+.gzi compressed files

bgzf-filehandle

add AbortController support to a cache of async requests

abortable-promise-cache

Parser for bigwig and bigbed files

bbi-js

A browser-based tool for the visual comparison of various maps (sequence, genetic, etc.) from any number of species.

cmap

A parser for the BED format including autoSql support

bed-js

read and write UCSC track and assembly hub files in node or the browser

ucsc-hub-js

JBrowse 2 plugin for integrating with GDC resources

jbrowse-plugin-gdc

use a subset of the NodeJS promise-based file handle API to access both local and remote files

generic-filehandle

Read .2bit files with pure JS. Works in node or webpack.

twobit-js

JBrowse/Galaxy-Blast Plugin

jblast-jbconnect-hook

CSS

mimosa

Miniature Model Organism Sequence Aligner

CSS

jbrowse-plugin-template

Template to quickly start a new JBrowse 2 plugin

jbrowse-docker

JBrowse docker project

Shell

ixixx-js

multiple sequence alignment browser plugin for JBrowse 2

jbrowse-plugin-msaview

JBrowse 2 plugin for editing annotations on an Apollo server

Apollo3

List of plugins for the JBrowse 2 plugin store.

jbrowse-plugin-list

jbrowse-plugin-ideogram

JBrowse 2 plugin for rendering ideograms

Index a FASTA file similar to `samtools faidx` using pure js

faidx-js

display a graphical summary of a BLAST report

Bio-GMOD-Blast-Graph

Read htsjdk tribble indexes in pure JS

tribble-index-js

nodejs-based server for handling usage reports coming in from JBrowse instances

jbrowse_analytics

Repo for storing dockerfile and config for a coronavirus genome browser

sars-cov-2-jbrowse

Dockerfile

gtf-js

GTF parsing library in JavaScript

Genome projection library

genome-projection

Groovy

jbrowse-plugin-quantseq

External JB2 plugin implementing a QuantitativeSequence track for displaying base-resolution models.

JBrowse 2 plugin integrating with Reactome

jbrowse-plugin-reactome

A CLI program to generate static image exports for jb2

jb2export

JBConnect, an optional server-side component of JBrowse

jbconnect

a web interface for setting up GBrowse instances

WebGBrowse

jb2profile