andersen-lab/bjorn issues and pull requests

#50 - SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly

Issue - State: closed - Opened by thomasbtf almost 3 years ago - 4 comments

#49 - Optimize OR queries for WHO lineages

Issue - State: open - Opened by flaneuse over 3 years ago
Labels: enhancement

#48 - Bjorn logo 1

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

#47 - Bjorn needs setup.py so that bjorn_utils can import

Issue - State: open - Opened by kramesh1 over 3 years ago - 1 comment
Labels: enhancement

#46 - Hashtables for caching and analysis

Issue - State: open - Opened by mindoftea over 3 years ago
Labels: enhancement, performance

#45 - Documentation out of date

Issue - State: open - Opened by mindoftea over 3 years ago
Labels: documentation

#44 - out-of-frame substitutions follow deletion-based codon numbering

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

#44 - out-of-frame substitutions follow deletion-based codon numbering

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

#43 - Out of frame deletions in B.1.1.7 followed by erroneous mutations

Issue - State: closed - Opened by gkarthik over 3 years ago - 1 comment
Labels: bug

#42 - NCBI Upload Pipe

Pull Request - State: closed - Opened by kramesh1 over 3 years ago - 2 comments

#41 - Split Pipeline and Outbreak.info code in Bjorn repo

Issue - State: closed - Opened by kramesh1 over 3 years ago - 3 comments
Labels: documentation, enhancement

#38 - Post inspection automation workflow in python

Pull Request - State: closed - Opened by kramesh1 over 3 years ago - 3 comments
Labels: enhancement

#35 - Streamline metadata interaction

Pull Request - State: closed - Opened by kramesh1 over 3 years ago - 3 comments

#34 - pangolin dependency not available in v2.3.2, datafunk not available in v0.0.8

Issue - State: closed - Opened by kramesh1 over 3 years ago - 3 comments
Labels: bug

#34 - pangolin dependency not available in v2.3.2, datafunk not available in v0.0.8

Issue - State: closed - Opened by kramesh1 over 3 years ago - 3 comments
Labels: bug

#32 - Auto-generation of updated README during release pipeline

Issue - State: closed - Opened by kramesh1 over 3 years ago - 1 comment
Labels: enhancement

#29 - Add second check for no insertions

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

#28 - Issue27 fix

Pull Request - State: open - Opened by AlaaALatif over 3 years ago

#27 - Implement corrected Deletion naming after PR #24

Issue - State: closed - Opened by AlaaALatif over 3 years ago - 3 comments
Labels: mutations

#26 - Calculate insertions

Issue - State: open - Opened by flaneuse over 3 years ago
Labels: enhancement, mutations

#26 - Calculate insertions

Issue - State: open - Opened by flaneuse over 3 years ago
Labels: enhancement, mutations

#25 - update from main

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

#24 - Issue22 fix

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

#23 - Austria geo normalization issues

Issue - State: open - Opened by flaneuse over 3 years ago
Labels: geo-normalization

#22 - Count mutations produced by out-of-frame deletions

Issue - State: closed - Opened by gkarthik over 3 years ago

#21 - Standardize position numbering with out-of-frame deletions

Issue - State: closed - Opened by gkarthik over 3 years ago

#20 - Store sequences with Ns in positions with mutations

Issue - State: open - Opened by gkarthik over 3 years ago - 9 comments
Labels: enhancement, mutations

#19 - Improve county-level normalization

Issue - State: open - Opened by flaneuse over 3 years ago
Labels: geo-normalization

#19 - Improve county-level normalization

Issue - State: open - Opened by flaneuse over 3 years ago
Labels: geo-normalization

#18 - Maintenance I

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

#17 - Translate non-ascii characters in location names to ascii for ease of parsing

Issue - State: open - Opened by gkarthik over 3 years ago
Labels: geo-normalization

#16 - BUG: England not displayed in location lookup

Issue - State: open - Opened by flaneuse over 3 years ago
Labels: geo-normalization

#15 - Bjorn1 sitrep

Pull Request - State: open - Opened by AlaaALatif over 3 years ago

#14 - Add pangolin lineage calls to pipeline

Issue - State: open - Opened by gkarthik almost 4 years ago
Labels: enhancement, feature

#13 - fix puerto rico location normalization

Pull Request - State: closed - Opened by AlaaALatif almost 4 years ago

#12 - Further Swiss Normalization fixes

Pull Request - State: closed - Opened by corneliusroemer almost 4 years ago

#11 - Fixed Swiss normalisation for GADM

Pull Request - State: closed - Opened by corneliusroemer almost 4 years ago - 2 comments

#10 - Swiss fix

Pull Request - State: closed - Opened by corneliusroemer almost 4 years ago

#9 - Bjorn1 sitrep

Pull Request - State: closed - Opened by AlaaALatif almost 4 years ago

#8 - How is location name matching to ISO-3166 codes done?

Issue - State: closed - Opened by corneliusroemer almost 4 years ago - 9 comments

#7 - Normalised Admin1 Switzerland

Pull Request - State: closed - Opened by corneliusroemer almost 4 years ago - 6 comments

#6 - Bjorn1

Pull Request - State: closed - Opened by AlaaALatif almost 4 years ago

#5 - Bjorn1

Pull Request - State: closed - Opened by AlaaALatif almost 4 years ago - 1 comment

#4 - Bjorn1

Pull Request - State: closed - Opened by AlaaALatif almost 4 years ago

#3 - Dev

Pull Request - State: closed - Opened by AlaaALatif almost 4 years ago

#2 - Bjorn: Add tutorial notebooks for using Bjorn's support functions

Issue - State: closed - Opened by AlaaALatif almost 4 years ago
Labels: documentation, enhancement

#1 - Genomic Surveillance: replace datafunk's sam_2_fasta with gofasta

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

GitHub / andersen-lab/bjorn issues and pull requests