Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of https://github.com/cidgoh/virus-mvp

https://github.com/cidgoh/virus-mvp - v1.0.0-no-upload

What's Changed

  • Download mutation index JSON by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/221
  • More informative interface by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/222

Full Changelog: https://github.com/cidgoh/VIRUS-MVP/compare/v0.12.1-no-upload...v1.0.0-no-upload

- Python
Published by ivansg44 11 months ago

https://github.com/cidgoh/virus-mvp - v1.0.0

What's Changed

  • Download mutation index JSON by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/221
  • More informative interface by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/222

Full Changelog: https://github.com/cidgoh/VIRUS-MVP/compare/v0.12.1...v1.0.0

- Python
Published by ivansg44 11 months ago

https://github.com/cidgoh/virus-mvp - v0.12.1-no-upload

What's Changed

  • Parse latest nf-ncov-voc genome config format by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/220

Full Changelog: https://github.com/cidgoh/VIRUS-MVP/compare/v0.12.0-no-upload...v0.12.1-no-upload

- Python
Published by ivansg44 over 1 year ago

https://github.com/cidgoh/virus-mvp - v0.12.1

What's Changed

  • Parse latest nf-ncov-voc genome config format by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/220

Full Changelog: https://github.com/cidgoh/VIRUS-MVP/compare/v0.12.0...v0.12.1

- Python
Published by ivansg44 over 1 year ago

https://github.com/cidgoh/virus-mvp - v0.12.0-no-upload

What's Changed

  • Parse new GVF format by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/214
  • Only download visible group surveillance reports by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/215
  • Fix broken default generator script by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/216
  • Update nf-ncov-voc to latest by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/217

Full Changelog: https://github.com/cidgoh/VIRUS-MVP/compare/v0.11.1-no-upload...v0.12.0-no-upload

- Python
Published by ivansg44 over 1 year ago

https://github.com/cidgoh/virus-mvp - v0.12.0

What's Changed

  • Parse new GVF format by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/214
  • Only download visible group surveillance reports by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/215
  • Fix broken default generator script by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/216
  • Update nf-ncov-voc to latest by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/217

Full Changelog: https://github.com/cidgoh/VIRUS-MVP/compare/v0.11.1...v0.12.0

- Python
Published by ivansg44 over 1 year ago

https://github.com/cidgoh/virus-mvp - 0.11.1 - no upload functionality

What's Changed

  • Parse n/a fn vals in gvf by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/213

Full Changelog: https://github.com/cidgoh/VIRUS-MVP/compare/v0.11.0-no-upload...v0.11.1-no-upload

- Python
Published by ivansg44 about 2 years ago

https://github.com/cidgoh/virus-mvp - 0.11.1

What's Changed

  • Parse n/a fn vals in gvf by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/213

Full Changelog: https://github.com/cidgoh/VIRUS-MVP/compare/v0.11.0...v0.11.1

- Python
Published by ivansg44 about 2 years ago

https://github.com/cidgoh/virus-mvp - 0.11.0 - no upload functionality

What's Changed

  • Improved docker image by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/206
  • Stop hidden strains from defaulting when none hidden by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/210
  • Change select groups modal loading behaviour by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/208
    • Opens much faster with large datasets

Full Changelog: https://github.com/cidgoh/VIRUS-MVP/compare/v0.10.0-no-upload...v0.11.0-no-upload

- Python
Published by ivansg44 about 2 years ago

https://github.com/cidgoh/virus-mvp - 0.11.0

What's Changed

  • Improved docker image by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/206
    • nf-ncov-voc now uses docker profile instead of conda
  • Stop hidden strains from defaulting when none hidden by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/210
  • Change select groups modal loading behaviour by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/208
    • Opens much faster with large datasets

Full Changelog: https://github.com/cidgoh/VIRUS-MVP/compare/v0.10.0...v0.11.0

- Python
Published by ivansg44 about 2 years ago

https://github.com/cidgoh/virus-mvp - v0.10.0-no-upload

What's Changed

  • Scroll heatmap to S gene on page launch by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/178
  • Force heatmap tick angles to 90 by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/179
  • NSP bar fig update callback by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/182
  • Become VIRUS-MVP by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/189
  • Display top 100 lineages by default by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/193
  • Fetch latest resources for defaults generator by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/194
  • Surface level vocabulary generalization by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/199
  • Process new gvf format by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/195

Full Changelog: https://github.com/cidgoh/VIRUS-MVP/compare/v0.9.0-no-upload...v0.10.0-no-upload

- Python
Published by ivansg44 about 2 years ago

https://github.com/cidgoh/virus-mvp - v0.10.0

What's Changed

  • Scroll heatmap to S gene on page launch by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/178
  • Force heatmap tick angles to 90 by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/179
  • NSP bar fig update callback by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/182
  • Become VIRUS-MVP by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/189
  • Display top 100 lineages by default by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/193
  • Fetch latest resources for defaults generator by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/194
  • Surface level vocabulary generalization by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/199
  • Process new gvf format by @ivansg44 in https://github.com/cidgoh/VIRUS-MVP/pull/195

Full Changelog: https://github.com/cidgoh/VIRUS-MVP/compare/v0.9.0-no-upload...v0.10.0

- Python
Published by ivansg44 about 2 years ago

https://github.com/cidgoh/virus-mvp - 0.9.0 - no upload functionality

Notable changes

  • #168 - Heterozygous mutations are encoded as consistent positions within columns
  • #169 - Updated data, and show only a subset of lineages by default

- Python
Published by ivansg44 about 3 years ago

https://github.com/cidgoh/virus-mvp - 0.9.0

Notable changes

  • #168 - Heterozygous mutations are encoded as consistent positions within columns
  • #169 - Updated data, and show only a subset of lineages by default

- Python
Published by ivansg44 about 3 years ago

https://github.com/cidgoh/virus-mvp - 0.8.0 - no upload functionality

Notable changes

  • #156 - Simpler docker setup
  • #157 - Successful parsing of multi allele mutations

- Python
Published by ivansg44 over 3 years ago

https://github.com/cidgoh/virus-mvp - 0.8.0

Notable changes

  • #156 - Simpler docker setup
  • #157 - Successful parsing of multi allele mutations

- Python
Published by ivansg44 over 3 years ago

https://github.com/cidgoh/virus-mvp - 0.7.0 - no upload functionality

Notable changes

  • #141 - Ability to jump through the heatmap by:
    • Clicking on a region in the gene bar under the histogram
    • Selecting a mutation from the "Jump to..." modal
  • #145 - Visually encode actively circulating lineages
  • #148 and #149 - NSP bar under heatmap gene bar
Other changes
  • #139 - More obvious help button
  • #143 - Larger minimum heatmap size, to prevent hover-boxes from occasionally disappearing
  • #155 - Order lineages by whether they are actively circulating, then variant, then lineage name

- Python
Published by ivansg44 over 3 years ago

https://github.com/cidgoh/virus-mvp - 0.7.0

Notable changes

  • #141 - Ability to jump through the heatmap by:
    • Clicking on a region in the gene bar under the histogram
    • Selecting a mutation from the "Jump to..." modal
  • #145 - Visually encode actively circulating lineages
  • #148 and #149 - NSP bar under heatmap gene bar
Other changes
  • #139 - More obvious help button
  • #143 - Larger minimum heatmap size, to prevent hover-boxes from occasionally disappearing
  • #155 - Order lineages by whether they are actively circulating, then variant, then lineage name

- Python
Published by ivansg44 over 3 years ago

https://github.com/cidgoh/virus-mvp - 0.7.0-alpha

Notable changes

  • #141 - Ability to jump through the heatmap by:
    • Clicking on a region in the gene bar under the histogram
    • Selecting a mutation from the "Jump to..." modal
  • #145 - Updated genomic data, prepared on Jan 6 2022
  • #145 - Visually encode actively circulating lineages
Other changes
  • #139 - More obvious help button
  • #143 - Larger minimum heatmap size, to prevent hover-boxes from occasionally disappearing

@ivansg44 @anwarMZ

- Python
Published by ivansg44 over 3 years ago

https://github.com/cidgoh/virus-mvp - 0.6.2 - no upload functionality

Notable changes

  • #135 - Updated genomic data

- Python
Published by ivansg44 about 4 years ago

https://github.com/cidgoh/virus-mvp - 0.6.2

Notable changes

  • #135 - Updated genomic data

- Python
Published by ivansg44 about 4 years ago

https://github.com/cidgoh/virus-mvp - 0.6.1 - no upload functionality

Notable changes

  • #134 - Updated genomic data

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.6.1

Notable changes

134 - Updated genomic data

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.6.0 - no upload functionality

Notable changes

  • #131 - Updated genomic data
  • #132 - Incompatible API changes related to upload deletion function in versions with upload functionality

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.6.0

Notable changes

  • #131 - Updated genomic data
  • #132 - Allow users to delete uploads through the viz interface

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.5.0 - no upload functionality

Notable changes

  • #129 - Updated genomic data
  • #130 - Up-to-date surveillance reports are now automatically zipped for download

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.5.0

Notable changes

  • #128 - Fully integrate nf-ncov-voc pipeline into application interface
    • Uploading files now takes a little longer, but it actually runs the associated pipeline
  • #129 - Updated genomic data
  • #130 - Up-to-date surveillance reports are now automatically zipped for download

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.4.1 - no upload functionality

Notable changes

  • #127 - Fix bug preventing gene bar above heatmap from appearing beyond specific widths
  • #126 - Data update

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.4.1

Notable changes

  • #127 - Fix bug preventing gene bar above heatmap from appearing beyond specific widths
  • #126 - Data update

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.4.0 - no upload functionality

Notable changes

  • #99 - Slightly smaller font size and heatmap indel markers
  • #100 - New favicon and changed browser tab title to COVID-MVP
  • 81bdca33d09a8764d9ac282ef8223e40c51511ac - Annotation heatmap cells with associated functions using thicker borders
  • #102 - VOI and VOC in existing heatmap y-axis distinguished using italics and bold respectively
  • #103 - New heatmap y-axis for genomic analysis sample sizes
  • #104 - Existing and new legend material now in a div that appears after clicking a button
  • #109 - Buttons in select lineage modal for selecting and deselecting all strains in a directory
  • #112 - Cache lifespan extended from 5m to 1d
  • #114, #117 - Loading indicators

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.4.0

Notable changes

  • #99 - Slightly smaller font size and heatmap indel markers
  • #100 - New favicon and changed browser tab title to COVID-MVP
  • 81bdca33d09a8764d9ac282ef8223e40c51511ac - Annotation heatmap cells with associated functions using thicker borders
  • #102 - VOI and VOC in existing heatmap y-axis distinguished using italics and bold respectively
  • #103 - New heatmap y-axis for genomic analysis sample sizes
  • #104 - Existing and new legend material now in a div that appears after clicking a button
  • #109 - Buttons in select lineage modal for selecting and deselecting all strains in a directory
  • #112 - Cache lifespan extended from 5m to 1d
  • #114, #117 - Loading indicators

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.3.0 - no upload functionality

Application will now perform at similar speeds when run locally, and when deployed to a network.

Callbacks were modified to reduce the number of times the large, underlying data structure was passed between the front-end and back-end servers. Now, the data structure is cached on the back-end filesystem, and back-end callbacks are signalled by the front-end interface to access the cached structure directly.

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.3.0

Application will now perform at similar speeds when run locally, and when deployed to a network.

Callbacks were modified to reduce the number of times the large, underlying data structure was passed between the front-end and back-end servers. Now, the data structure is cached on the back-end filesystem, and back-end callbacks are signalled by the front-end interface to access the cached structure directly.

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.2.0 - no upload functionality

Ability to download surveillance reports

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.2.0

Ability to download surveillance reports

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.1.0 - no upload functionality

Initial release without upload functionality

- Python
Published by ivansg44 over 4 years ago

https://github.com/cidgoh/virus-mvp - 0.1.0

Initial release with upload functionality

- Python
Published by ivansg44 over 4 years ago