marianattestad/ribbon issues and pull requests

#123 - cram file support?

Issue - State: open - Opened by dnil 5 months ago - 15 comments

#100 - Bump d3-color and d3

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies

#99 - Update release notes and minor fixes

Pull Request - State: closed - Opened by MariaNattestad 5 months ago

#98 - Enable setting locus through the URL

Pull Request - State: closed - Opened by MariaNattestad 5 months ago

#97 - Move navbar items into tabs

Pull Request - State: closed - Opened by robertaboukhalil 5 months ago - 2 comments

#96 - Move sessions to the front page

Pull Request - State: closed - Opened by MariaNattestad 5 months ago

#95 - Rethink features and small variants in Ribbon

Issue - State: open - Opened by MariaNattestad 5 months ago

#94 - Documentation for v2.0.0 updates

Pull Request - State: closed - Opened by MariaNattestad 5 months ago

#93 - Update API to support v1.genomeribbon.com

Pull Request - State: closed - Opened by robertaboukhalil 5 months ago

#92 - Load sessions from URL

Pull Request - State: closed - Opened by robertaboukhalil 6 months ago

#91 - Color by HP tags

Pull Request - State: closed - Opened by MariaNattestad 6 months ago

#90 - Add examples, remove from gitignore.

Pull Request - State: closed - Opened by MariaNattestad 6 months ago

#89 - Move aioli and session loading to separate modules

Pull Request - State: closed - Opened by robertaboukhalil 6 months ago

#88 - Modernize JS and add more file loading from URLs

Pull Request - State: closed - Opened by MariaNattestad 6 months ago - 1 comment

#87 - Bring back sliders

Pull Request - State: closed - Opened by robertaboukhalil 6 months ago

#86 - visualize complex structural variants

Issue - State: closed - Opened by ywzhang071394 6 months ago - 3 comments

#85 - Add preset BAMs including GIAB HG008 tumor data.

Pull Request - State: closed - Opened by MariaNattestad 6 months ago

#84 - Load VCFs and other files from URLs

Issue - State: closed - Opened by robertaboukhalil 6 months ago

#83 - Overhaul Ribbon UI

Pull Request - State: closed - Opened by MariaNattestad 6 months ago - 1 comment

#82 - Remove warning about PG count

Pull Request - State: closed - Opened by robertaboukhalil 6 months ago

#81 - Add bcftools

Pull Request - State: closed - Opened by robertaboukhalil 6 months ago

#80 - Add bcftools

Pull Request - State: closed - Opened by robertaboukhalil 6 months ago

#79 - Fix duplicate HTML element IDs

Issue - State: closed - Opened by robertaboukhalil 6 months ago

#78 - Replace iobio for URL support

Pull Request - State: closed - Opened by robertaboukhalil 6 months ago - 3 comments

#77 - Potential improvements

Issue - State: open - Opened by robertaboukhalil 6 months ago

#76 - Initial cleanup part 2

Pull Request - State: closed - Opened by robertaboukhalil 6 months ago - 1 comment

#75 - Consolidate UI to connect Ribbon and SplitThreader

Issue - State: closed - Opened by MariaNattestad 6 months ago

#74 - Replace iobio for loading BAM URLs

Issue - State: closed - Opened by robertaboukhalil 6 months ago

#73 - Fix collapsible bug

Pull Request - State: closed - Opened by robertaboukhalil 6 months ago - 1 comment

#72 - Code cleanup

Issue - State: closed - Opened by robertaboukhalil 6 months ago

#71 - Initial cleanup

Pull Request - State: closed - Opened by robertaboukhalil 6 months ago - 1 comment

#70 - Look into supporting CNV calls

Issue - State: open - Opened by robertaboukhalil 6 months ago - 2 comments

#69 - Reference coordinates in the top and bottom views

Issue - State: open - Opened by robertaboukhalil 6 months ago

#68 - Support small chromosomes

Issue - State: open - Opened by robertaboukhalil 6 months ago

#67 - Documentation

Issue - State: closed - Opened by robertaboukhalil 6 months ago

#66 - Warn if reads are downsampled

Issue - State: closed - Opened by robertaboukhalil 6 months ago - 1 comment

#65 - Variants table: add scrollbar

Issue - State: closed - Opened by robertaboukhalil 6 months ago

#64 - Zoom in on part of a read

Issue - State: open - Opened by robertaboukhalil 6 months ago

#63 - Visualize multiple BAMs/VCFs

Issue - State: closed - Opened by robertaboukhalil 6 months ago - 2 comments

#62 - Visualize reads by haplotype

Issue - State: closed - Opened by robertaboukhalil 6 months ago

#61 - Update BED/VCF file without reloading the page

Issue - State: closed - Opened by robertaboukhalil 6 months ago - 1 comment

#60 - Load session JSON from a URL

Issue - State: closed - Opened by robertaboukhalil 6 months ago

#59 - Use VCF input instead of BEDPE

Issue - State: closed - Opened by robertaboukhalil 6 months ago

#58 - Bring SplitThreader into Ribbon

Issue - State: closed - Opened by robertaboukhalil 6 months ago - 2 comments

#57 - Remove backend from SplitThreader

Issue - State: closed - Opened by robertaboukhalil 6 months ago

#56 - Use static assets instead of CDN

Pull Request - State: closed - Opened by robertaboukhalil over 1 year ago - 1 comment

#55 - MUMmer does not identify regions from positive control samples

Issue - State: closed - Opened by s-t-calus about 2 years ago - 1 comment

#54 - Filtering reads with multi-read settings

Issue - State: closed - Opened by HannahJusten over 2 years ago - 5 comments

#53 - Bump moment from 2.29.3 to 2.29.4

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#52 - Upgrade to Aioli 3.0

Pull Request - State: closed - Opened by robertaboukhalil over 2 years ago

#51 - how to remove expand regions from selected region

Issue - State: closed - Opened by panxiaoguang over 2 years ago - 2 comments

#50 - Running Ribbon without internet access

Issue - State: closed - Opened by psammarco over 2 years ago - 16 comments

#49 - upload data from server

Issue - State: closed - Opened by jainy over 2 years ago - 1 comment

#48 - Update moment

Pull Request - State: closed - Opened by robertaboukhalil almost 3 years ago - 1 comment

#47 - [WIP] Update build script

Pull Request - State: closed - Opened by robertaboukhalil almost 3 years ago

#46 - Bump moment from 2.24.0 to 2.29.2

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 2 comments
Labels: dependencies

#45 - PG lines error although only one line contains the @PG header

Issue - State: closed - Opened by Estherrr1997 almost 3 years ago - 13 comments

#44 - load a bigger sam file

Issue - State: closed - Opened by anastasiiasatyr almost 3 years ago - 1 comment

#43 - Move permalink server

Pull Request - State: closed - Opened by robertaboukhalil over 3 years ago

#42 - Upgrade Ribbon to use Aioli 2.0.0

Pull Request - State: closed - Opened by robertaboukhalil over 3 years ago - 1 comment

#41 - Ribbon

Issue - State: closed - Opened by duhuipeng almost 4 years ago - 1 comment

#40 - Converting mummer alignment to bam, sam or coord-ITH format

Issue - State: closed - Opened by dieunelderilus about 4 years ago - 2 comments

#39 - Update package.json

Pull Request - State: closed - Opened by robertaboukhalil over 4 years ago - 1 comment

#38 - Update Ribbon version

Pull Request - State: closed - Opened by robertaboukhalil over 4 years ago

#37 - Fusions from Short Read Illumina Data

Issue - State: closed - Opened by jennylsmith over 4 years ago - 2 comments

#36 - Links Not Working on Linux

Issue - State: closed - Opened by taylorjtamu over 4 years ago - 2 comments

#35 - question about permalink configurations

Issue - State: closed - Opened by sdemirci over 4 years ago - 3 comments

#34 - Speed up time to retrieve reads from BAM files

Pull Request - State: closed - Opened by robertaboukhalil over 4 years ago - 1 comment

#33 - "Aw, Snap!" on Chrome

Issue - State: closed - Opened by francoiskroll over 4 years ago - 2 comments

#32 - Loading PacBio data

Issue - State: closed - Opened by plurie over 4 years ago - 1 comment

#31 - Bump jquery from 3.4.0 to 3.5.0

Pull Request - State: closed - Opened by dependabot[bot] almost 5 years ago
Labels: dependencies

#30 - genomeribbon.com down?

Issue - State: closed - Opened by conte1 almost 5 years ago - 2 comments

#29 - output file

Issue - State: closed - Opened by Br1anChou almost 5 years ago - 1 comment

#28 - Installation help

Issue - State: closed - Opened by cssulliv almost 5 years ago - 1 comment

#27 - Update Ribbon to use new iobio backend

Pull Request - State: closed - Opened by robertaboukhalil almost 5 years ago

#26 - Remove Ribbon's dependence on PHP

Pull Request - State: closed - Opened by robertaboukhalil almost 5 years ago - 1 comment

#25 - Scale chromosomes by size when viewing coordinates?

Issue - State: closed - Opened by conte1 almost 5 years ago - 1 comment

#24 - Optimize samtools .wasm

Pull Request - State: closed - Opened by robertaboukhalil about 5 years ago

#23 - Updated message system and feature selection

Pull Request - State: closed - Opened by MariaNattestad about 5 years ago

#22 - Bump bootstrap from 3.2.0 to 3.4.1

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago - 2 comments
Labels: dependencies

#21 - Bump jquery from 1.11.1 to 3.4.1

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago - 2 comments
Labels: dependencies

#20 - Use WebAssembly to parse local .bam files in the browser

Pull Request - State: closed - Opened by robertaboukhalil about 5 years ago

#19 - Pull Request: Use npm package.json

Pull Request - State: closed - Opened by robertaboukhalil over 5 years ago

#18 - unable to load BAM files

Issue - State: closed - Opened by hd00ljy about 6 years ago - 7 comments

#17 - error loading coords file

Issue - State: closed - Opened by rotifergirl about 6 years ago - 1 comment

#16 - why do bam files with multiple @PG header lines have been found to have issues fetching records.

Issue - State: closed - Opened by cangfengzhe over 6 years ago - 2 comments

#15 - how to get the gorilla_to_GRCh38 coords file just like in the website example?

Issue - State: closed - Opened by JiguangPeng almost 7 years ago

#14 - Error: File taking too long to load

Issue - State: closed - Opened by ghost almost 7 years ago - 2 comments

#13 - Ribbon on Linux

Issue - State: closed - Opened by catch-minie almost 7 years ago - 1 comment

#12 - Command line interface

Issue - State: closed - Opened by sjackman over 7 years ago - 6 comments

#11 - Add support for CSI BAM index files (REVIEW)

Pull Request - State: closed - Opened by nathanhaigh over 7 years ago - 2 comments

GitHub / marianattestad/ribbon issues and pull requests