jeromekelleher/sc2ts issues and pull requests

#100 - Classification for non-biological reversions

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 13 comments

#100 - Classification for non-biological reversions

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 13 comments

#99 - Update RecombinantAncestry.ipynb

Pull Request - State: open - Opened by hyanwong almost 2 years ago - 2 comments

#99 - Update RecombinantAncestry.ipynb

Pull Request - State: open - Opened by hyanwong almost 2 years ago - 2 comments

#98 - Add site_summary data frame

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 1 comment

#98 - Add site_summary data frame

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 1 comment

#97 - Add date_summary data frame

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 1 comment

#97 - Add date_summary data frame

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 1 comment

#96 - Fix #91

Pull Request - State: closed - Opened by hyanwong almost 2 years ago

#96 - Fix #91

Pull Request - State: closed - Opened by hyanwong almost 2 years ago

#95 - Classifying recombination nodes

Issue - State: open - Opened by hyanwong almost 2 years ago - 10 comments

#95 - Classifying recombination nodes

Issue - State: open - Opened by hyanwong almost 2 years ago - 10 comments

#94 - Classifying reversion mutations

Issue - State: open - Opened by hyanwong almost 2 years ago - 1 comment

#94 - Classifying reversion mutations

Issue - State: open - Opened by hyanwong almost 2 years ago - 1 comment

#93 - Add parameter search for recombinants

Issue - State: open - Opened by jeromekelleher almost 2 years ago

#93 - Add parameter search for recombinants

Issue - State: open - Opened by jeromekelleher almost 2 years ago

#92 - Mutations reported in copying pattern incorrect

Issue - State: open - Opened by jeromekelleher almost 2 years ago

#92 - Mutations reported in copying pattern incorrect

Issue - State: open - Opened by jeromekelleher almost 2 years ago

#91 - Three + parents broken in report

Issue - State: closed - Opened by jeromekelleher almost 2 years ago - 1 comment

#91 - Three + parents broken in report

Issue - State: closed - Opened by jeromekelleher almost 2 years ago - 1 comment

#90 - Validate by chunks

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#90 - Validate by chunks

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#89 - Change _copying_table to be horizontal & colour

Pull Request - State: closed - Opened by hyanwong almost 2 years ago

#89 - Change _copying_table to be horizontal & colour

Pull Request - State: closed - Opened by hyanwong almost 2 years ago

#88 - Add CLI for annotating recombinants with breakpoint info

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#88 - Add CLI for annotating recombinants with breakpoint info

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#87 - Fix missing nodes arg

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#87 - Fix missing nodes arg

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#86 - Reversion push code needs to deal with recombinants

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 2 comments

#86 - Reversion push code needs to deal with recombinants

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 2 comments

#85 - Create RecombinantAncestry.ipynb

Pull Request - State: closed - Opened by hyanwong almost 2 years ago

#85 - Create RecombinantAncestry.ipynb

Pull Request - State: closed - Opened by hyanwong almost 2 years ago

#84 - Use imputated pango if available

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#84 - Use imputated pango if available

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#83 - Fix bug in annotations

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#83 - Fix bug in annotations

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#82 - Add postprocess function to update "flagged" node times

Issue - State: open - Opened by jeromekelleher almost 2 years ago

#82 - Add postprocess function to update "flagged" node times

Issue - State: open - Opened by jeromekelleher almost 2 years ago

#81 - Ability not to filter out sites on intersection

Pull Request - State: closed - Opened by hyanwong almost 2 years ago - 3 comments

#81 - Ability not to filter out sites on intersection

Pull Request - State: closed - Opened by hyanwong almost 2 years ago - 3 comments

#80 - Node 1240908 incorrectly placed in upgma-full-md-30-mm-3-2021-06-30.ts.tsz

Issue - State: closed - Opened by jeromekelleher almost 2 years ago - 1 comment

#80 - Node 1240908 incorrectly placed in upgma-full-md-30-mm-3-2021-06-30.ts.tsz

Issue - State: closed - Opened by jeromekelleher almost 2 years ago - 1 comment

#79 - Some branch lengths systematically too long

Issue - State: open - Opened by jeromekelleher almost 2 years ago

#79 - Some branch lengths systematically too long

Issue - State: open - Opened by jeromekelleher almost 2 years ago

#78 - Don't import tsconvert

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#78 - Don't import tsconvert

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#77 - Ways to correct "myopic" tree building

Issue - State: open - Opened by hyanwong almost 2 years ago - 1 comment

#77 - Ways to correct "myopic" tree building

Issue - State: open - Opened by hyanwong almost 2 years ago - 1 comment

#76 - Site utils

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#76 - Site utils

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#75 - Add nextstrain colours

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

#75 - Add nextstrain colours

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

#74 - Functions to extract the nextstrain nexus files

Pull Request - State: closed - Opened by hyanwong almost 2 years ago

#74 - Functions to extract the nextstrain nexus files

Pull Request - State: closed - Opened by hyanwong almost 2 years ago

#73 - Add cophylogeny notebook

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

#73 - Add cophylogeny notebook

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

#72 - Rename nextstrain JSON functions to "nextclade"

Pull Request - State: closed - Opened by hyanwong almost 2 years ago

#72 - Rename nextstrain JSON functions to "nextclade"

Pull Request - State: closed - Opened by hyanwong almost 2 years ago

#71 - Adds genes to plots

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#71 - Adds genes to plots

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#70 - Nextstrain tree only contains intergenic mutations

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 2 comments

#70 - Nextstrain tree only contains intergenic mutations

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 2 comments

#69 - Lineage imputation

Pull Request - State: closed - Opened by a-ignatieva almost 2 years ago - 1 comment

#69 - Lineage imputation

Pull Request - State: closed - Opened by a-ignatieva almost 2 years ago - 1 comment

#68 - Plot of dN/dS along the genome

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 1 comment

#68 - Plot of dN/dS along the genome

Issue - State: open - Opened by jeromekelleher almost 2 years ago - 1 comment

#67 - Add private mutations to reports

Issue - State: closed - Opened by jeromekelleher almost 2 years ago

#67 - Add private mutations to reports

Issue - State: closed - Opened by jeromekelleher almost 2 years ago

#66 - Lineage imputation and sample subgraph plots

Pull Request - State: closed - Opened by a-ignatieva almost 2 years ago - 5 comments

#66 - Lineage imputation and sample subgraph plots

Pull Request - State: closed - Opened by a-ignatieva almost 2 years ago - 5 comments

#65 - Nextstrain utilities

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#65 - Nextstrain utilities

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#64 - Add genes to plots

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#64 - Add genes to plots

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#63 - Generalise inspection code

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#63 - Generalise inspection code

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#62 - Improvements to recombinant handling

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#62 - Improvements to recombinant handling

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#61 - Remove extra code that snuck in

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#61 - Remove extra code that snuck in

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#60 - Fix error in recombinants per day plot

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#60 - Fix error in recombinants per day plot

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#59 - recombinants plot broken

Issue - State: closed - Opened by jeromekelleher almost 2 years ago

#59 - recombinants plot broken

Issue - State: closed - Opened by jeromekelleher almost 2 years ago

#58 - Inspect recombinant

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#58 - Inspect recombinant

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#57 - Minor tweaks to utils

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#56 - Fixup some broken analysis code by change of metadata

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#56 - Fixup some broken analysis code by change of metadata

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#55 - Revert to scipy-based UPGMA tree

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#55 - Revert to scipy-based UPGMA tree

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#54 - Local tsinfer

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago - 1 comment

#54 - Local tsinfer

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago - 1 comment

#53 - Update metadata for added nodes.

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#53 - Update metadata for added nodes.

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#52 - Build local trees using maximum parismony

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#52 - Build local trees using maximum parismony

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#51 - Recombinant lineages report

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#51 - Recombinant lineages report

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

#50 - More utils

Pull Request - State: closed - Opened by jeromekelleher almost 2 years ago

GitHub / jeromekelleher/sc2ts issues and pull requests