strchive - v2.9.1

What's Changed

Minor Changes

Locus updates

• Score tags update by @Macayla-weiner in https://github.com/dashnowlab/STRchive/pull/259

Website and repository updates

• loci table changes by @vincerubinetti in https://github.com/dashnowlab/STRchive/pull/256
• Fix plots not updating in PRs by @hdashnow in https://github.com/dashnowlab/STRchive/pull/257 and https://github.com/dashnowlab/STRchive/pull/253

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.9.0...v2.9.1

- Python
Published by github-actions[bot] 7 months ago

strchive - v2.9.0

What's Changed

Locus updates

• July lit update by @Macayla-weiner in https://github.com/dashnowlab/STRchive/pull/248

Major Changes

• PLIN4 pathogenic min decreased from 39 to 37

Minor Changes

• Minor update to SCA3
• PLIN4 pathogenic min, age onset upper bound, and ancestry details updated
• FRDA description updated

Website updates

• Tidy up filters on loci page by @vincerubinetti in https://github.com/dashnowlab/STRchive/pull/250
• upgrade package versions by @vincerubinetti in https://github.com/dashnowlab/STRchive/pull/251

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.8.0...v2.9.0

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Published by github-actions[bot] 7 months ago

strchive - v2.8.0

What's Changed

Locus updates

• Loci are now tagged with their current manual review status @Macayla-weiner in https://github.com/dashnowlab/STRchive/pull/229

Website updates

• Contact form by @vincerubinetti in https://github.com/dashnowlab/STRchive/pull/242
• Update Literature by @github-actions[bot] in https://github.com/dashnowlab/STRchive/pull/243

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.7.0...v2.8.0

- Python
Published by github-actions[bot] 7 months ago

strchive - v2.7.0

What's Changed

Major

Locus updates

• The pre-MIR7-2 gene was renamed to MIR7-2 (the official HGNC symbol) by @hdashnow in https://github.com/dashnowlab/STRchive/pull/236

Website updates

• Added Locus page links to two new resources:
  • DECIPHER by @hdashnow in https://github.com/dashnowlab/STRchive/pull/236
  • TR Explorer by @hdashnow in https://github.com/dashnowlab/STRchive/pull/234

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.6.0...v2.7.0

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Published by github-actions[bot] 8 months ago

strchive - v2.6.0

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Published by github-actions[bot] 8 months ago

strchive - v2.5.1

What's Changed

• Update Literature by @Macayla-weiner in #217 and #220

Minor Changes

• SAMD12 age of onset lower bound was updated from 12 to 8 years
• PLIN4 ID was fixed to be MRUPAVPLIN4 rather than PLIN4MRUPAV
• PLIN4 description fixed

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.5.0...v2.5.1

- Python
Published by github-actions[bot] 8 months ago

strchive - v2.5.0

What's Changed

Major

New loci:

• RUNX2 by @Macayla-weiner in https://github.com/dashnowlab/STRchive/pull/214
• TYMS by @Macayla-weiner in https://github.com/dashnowlab/STRchive/pull/212
• PLIN4 by @Macayla-weiner in https://github.com/dashnowlab/STRchive/pull/193

Major locus updates:

• MUC1 - remove pathogenic range and present as a motif switch instead by @hdashnow in https://github.com/dashnowlab/STRchive/pull/211
• MUC1 Update by @Macayla-weiner in https://github.com/dashnowlab/STRchive/pull/202

STRchive general updates:

• Add JSON schema for STRchive-loci.json by @hdashnow in https://github.com/dashnowlab/STRchive/pull/126

Minor

• allow locus_structure to be null in trgt script by @hdashnow in https://github.com/dashnowlab/STRchive/pull/208
• Fetch full citation for new references in PRs using manubot by @hdashnow in https://github.com/dashnowlab/STRchive/pull/210
• increment version and update plots and literature by @hdashnow in https://github.com/dashnowlab/STRchive/pull/216

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.4.4...v2.5.0

- Python
Published by github-actions[bot] 8 months ago

strchive - v2.4.4

What's Changed

• Renamed some OPDM loci to improve consistency
• June literature review by @Macayla-weiner https://github.com/dashnowlab/STRchive/pull/194
• Update Literature by @github-actions in https://github.com/dashnowlab/STRchive/pull/187
• sentence case for "type" diseases (SCA, DM1/DM2) by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/188

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.4.3...v2.4.4

- Python
Published by github-actions[bot] 9 months ago

strchive - v2.4.3

What's Changed

• May Lit Review by @Macayla-weiner, including:
  • https://github.com/dashnowlab/STRchive/pull/182
  • https://github.com/dashnowlab/STRchive/pull/177
  • https://github.com/dashnowlab/STRchive/pull/179
• add STRchive paper to README and citation file by @hdashnow in https://github.com/dashnowlab/STRchive/pull/176

Minor locus updates:

• Japanese and Chinese cohorts added to OPDM
• Noted mechanism for ASD mimicking splicing in DM1
• Noted association between DM1 and ASD/related traits
• Added Italian cohort for SCA27B
• Fixed typo in HTT: associated vs assocated
• Noted JPH3 founder mutation in African ancestry
• SCA4 age of onset extended to 12 - 65

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.4.2...v2.4.3

- Python
Published by github-actions[bot] 10 months ago

strchive - v2.4.2

What's Changed

• Update Literature by @github-actions in https://github.com/dashnowlab/STRchive/pull/170

This PR introduces changes from automated literature retrieval followed by manual curation.

Minor Changes

• Extend age of onset range for TCF4
• New regional cohort for Kennedy Disease (AR)

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.4.1...v2.4.2

- Python
Published by github-actions[bot] 11 months ago

strchive - v2.4.1

What's Changed

Major

• Major coordinate updates based on feedback from @penhoorn at PacBio by @hdashnow in https://github.com/dashnowlab/STRchive/pull/155
• Extract reference allele for each locus by @avvaruakshay
• March 2025 literature updates by @laurelhiatt and @hdashnow in https://github.com/dashnowlab/STRchive/pull/169

Minor

• Remove space from downloaded file names by @hdashnow in https://github.com/dashnowlab/STRchive/pull/159
• update from preprint to paper! by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/168
• add abcd3 typ age onset range by @hdashnow in https://github.com/dashnowlab/STRchive/pull/172

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.3.1...v2.4.1

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Published by github-actions[bot] 11 months ago

strchive - v2.3.1

What's Changed

• Script to display ref alleles for all loci by @hdashnow and @avvaruakshay in https://github.com/dashnowlab/STRchive/pull/154
• updating intermediate range for SCA6 by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/161

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.2.1...v2.3.1

- Python
Published by github-actions[bot] about 1 year ago

strchive - v2.2.1

What's Changed

• add explanation text as static element by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/143
• add 1 to start position in UCSC links by @hdashnow in https://github.com/dashnowlab/STRchive/pull/151
• Update Literature by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/147
  • Adding details of phenotypic spectra to DIP2B and RFC1 loci
  • Adding new youngest age to MUC1, as well as citation supporting difficulty genotyping

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.2.0...v2.2.1

- Python
Published by github-actions[bot] about 1 year ago

strchive - v2.2.0

What's Changed

Locus changes * Fix NAXE chr 15 -> 1 and update coordinates by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/142

Website and workflow changes * Time stamp updates for each locus in STRchive-loci.json by @hdashnow in https://github.com/dashnowlab/STRchive/pull/139 * Add PR templates for general and Literature PRs by @hdashnow in https://github.com/dashnowlab/STRchive/pull/138

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.1.0...v2.2.0

- Python
Published by github-actions[bot] about 1 year ago

strchive - v2.1.0

What's Changed

• gnomAD plots of "pathogenic genotype" frequency added for a subset of loci by @avvaruakshay #123 #127 #128
• Automation of monthly literature updates using GitHub Actions by @hdashnow #134
• Disease locus literature updates by @laurelhiatt and @hdashnow #133 #136
• Minor fixes #131

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v2.0.1...v2.1.0

- Python
Published by github-actions[bot] about 1 year ago

strchive - v2.0.1

We have substantially updated the STRchive website interface to be more user-friendly and informative. Citations are now available for each discrete data point, rather than associated with locus pages, to facilitate the transparency of our descriptions and conclusions. Additionally, we have added resources to allow STRchive to be maintained as a living resource, including automated literature queries and ongoing expert curation.

What's Changed

• Major website redesign by @vincerubinetti
• Genes added since the last release: MUC1, NAXE, pre-MIR7-2 by @laurelhiatt and @hdashnow
• Breaking change: an overhaul of the data format. The STRchive loci are now stored in data/STRchive-loci.json with updated field names and no csv format. See #44 #95 and #26 by @hdashnow
• Clearer data to citation associations and referencing with manubot by @vincerubinetti and @laurelhiatt
• Enhanced automated literature retrieval by @laurelhiatt
• Population frequency of "pathogenic genotypes" by @avvaruakshay and @laurelhiatt

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v1.2.0...v2.0.1

- Python
Published by github-actions[bot] about 1 year ago

strchive - v1.2.0

What's Changed

New loci: * new locus: RAI1 by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/48 * Add TAF1 XDP by @hdashnow in https://github.com/dashnowlab/STRchive/pull/43

Locus updates: * update SCA10 GeneReview by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/30 * FGF14 update by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/29

New data added for most loci: * updated data from recent lit by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/33 * TR-gnomAD IDs added by @hdashnow in https://github.com/dashnowlab/STRchive/pull/41 * Disease descriptions by @hdashnow in https://github.com/dashnowlab/STRchive/pull/35 * clinical disease description edits by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/42 * added TR-gnomAD and Webstr IDs by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/45 * Gene pages: add descriptions and TR-gnomAD by @hdashnow in https://github.com/dashnowlab/STRchive/pull/46 * Malacards by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/51 * gene locations taken from NBK535148, UCSC Genome Browser on Human (GR… by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/52 * Ancestry by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/50

Minor edits and fixes: * GLS Mondo code lacked first 0 by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/31 * * fixed GARD FAME bug by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/47

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v1.1.0...v1.2.0

- Python
Published by hdashnow over 1 year ago

strchive - v1.1.0

What's Changed

• updating AR and ARX by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/23
• Update STRchive-database.json for DAB1 by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/27
• Mondo terms added by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/28
• Add links to useful TR catalogs under Resources
• Fix TRGT bed file download links

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v1.0.0...v1.1.0

- Python
Published by hdashnow over 1 year ago

strchive - v1.0.0 Preprint release

This STRchive version corresponds to the preprint release

What's Changed

• Prevalence updates
• Addition of automated citation data to website
• Website formatting

PRs since last version

• Missednotypicalages by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/13
• update motif and add detail by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/15
• Prevalence recheck by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/16
• Motifsfromreview by @laurelhiatt in https://github.com/dashnowlab/STRchive/pull/19

Full Changelog: https://github.com/dashnowlab/STRchive/compare/v0.2.0...v1.0.0

- Python
Published by hdashnow almost 2 years ago

strchive - v0.2.0

What's Changed

• Renamed and sorted the underlying database and updated how we manage collaborative edits by @hdashnow. See https://github.com/hdashnow/STRchive/pull/12 (Note: non-backwards-compatible!)
• Major age of onset updates and more details by @laurelhiatt in https://github.com/hdashnow/STRchive/pull/8 and https://github.com/hdashnow/STRchive/pull/11
• General tidy and update to the website and plots

Full Changelog: https://github.com/hdashnow/STRchive/compare/v0.1.0...v0.2.0

- Python
Published by hdashnow almost 2 years ago

strchive - v0.1.0

Initial release of STRchive!

Full Changelog: https://github.com/hdashnow/STRchive/commits/v0.1.0

- Python
Published by hdashnow about 2 years ago