Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / jbloomlab/polyclonal issues and pull requests

#187 - Fix bug in plotting `minimum max of <stat> at site slider`

Pull Request - State: closed - Opened by jbloom about 2 months ago

#186 - define per-model regions in `PolyclonalCollection` (for averaging)

Pull Request - State: closed - Opened by jbloom about 2 months ago

#184 - update doc links to new Bloom lab webpage

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

#183 - add `mean_abs` and `sum_abs` to `lineplot_and_heatmap`

Pull Request - State: closed - Opened by jbloom about 1 year ago

#182 - improve stat hiding filters in `lineplot_and_heatmap`

Pull Request - State: closed - Opened by jbloom about 1 year ago

#181 - Added `rename_std` option to `lineplot_and_heatmaps`

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

#179 - enabling filtering of plots by standard deviation of measurements

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

#177 - improve heatmap limits

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

#176 - heatmap shows as grayed out filtered mutations even w no escape measured

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

#175 - add `min_times_seen` to `PolyclonalCollection.mut_escape_corr`

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

#174 - fix `mut_icXX` bug and increase bounds

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

#172 - switch to testing via GitHub Actions rather than Travis

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

#171 - ensure `PolyclonalCollection.sites` is always defined

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

#170 - correct implementation of `check_wt_icXX` (becomes version 6.2)

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

#169 - expand `icXX` methods range

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

#168 - check_wt_icXX lower bound is too restrictive for potent sera

Issue - State: closed - Opened by fwelsh over 1 year ago - 6 comments

#167 - add `PolyclonalCollection.mut_icXX_*` methods

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

#166 - Add `mut_icXX_plot` and `mut_icXX_df` methods to `Polyclonal`.

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

#165 - change linting from `flake8` to `ruff`

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

#164 - upgrade minimum `altair` to 5.0.0

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

#163 - add "min_magnitude" `avg_type` for mut escape in `PolyclonalCollection`

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

#162 - fold change ICXX plots

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

#161 - using spacial distances masks some escape sites

Issue - State: open - Opened by Bernadetadad almost 2 years ago - 7 comments

#160 - use `altair` version 5.0

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

#159 - increase default `reg_activity_weight` from 1.0 to 2.0

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

#158 - fit model with fixed Hill coefficient and non-neutralized fraction first

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

#157 - change Hill coefficient regularization

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

#156 - bounds to `Polyclonal.fit` as params rather than harcoded

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

#155 - Remove `is_weighted_replicate` from `curves_plot` tooltip

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

#153 - Add option to exclude a list of sites from escape plotting

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

#151 - generalize Hill curves (version 4.0)

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

#150 - epitope colours

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

#149 - default fitting parameters?

Issue - State: closed - Opened by jbloom almost 2 years ago - 6 comments

#148 - improve plotting and allow heatmaps to hide rather than filter mutations

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

#147 - Show heatmap tooltip null numerical values as NaN

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

#146 - visualize per-model measurements for averages of models

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

#145 - enable user-specified fixed limits on heatmap ranges

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

#144 - enable visualization of filtered mutations

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

#143 - Allow cif files for PDB structures

Issue - State: closed - Opened by Bernadetadad about 2 years ago - 1 comment

#142 - customization options for escape plotting

Pull Request - State: closed - Opened by jbloom about 2 years ago - 1 comment

#140 - Allow str site numbers in `reassign_b_factor` (v 3.2)

Pull Request - State: closed - Opened by jbloom about 2 years ago

#139 - Allow non-int site numbers in PDB b-factor reassignment

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

#138 - Change default positive colors

Pull Request - State: closed - Opened by timcyu about 2 years ago - 3 comments

#137 - Epitope colors for polyclonal

Issue - State: closed - Opened by timcyu about 2 years ago - 6 comments

#136 - version 3.0: adjust regularization weights, add examples

Pull Request - State: closed - Opened by jbloom about 2 years ago - 2 comments

#135 - implementation of uniqueness regularization

Pull Request - State: closed - Opened by jbloom about 2 years ago

#134 - implement spatial regularization

Pull Request - State: closed - Opened by jbloom about 2 years ago

#133 - flatten escape values at near-zero sites in RBD simulated data

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

#132 - Epitopes are questionably separated despite the epitope similarity penalty

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

#131 - fix assert statement in reg_similarity

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

#130 - implement epitope similarity regularization with absolute value approximation

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

#129 - fix bug in wildtype heatmap plot introduced in 2.3

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

#128 - implement epitope similarity regularization

Pull Request - State: closed - Opened by timcyu over 2 years ago - 8 comments

#126 - allow `data_mut_escape_overlap` != "exact" even with `sites` set

Pull Request - State: closed - Opened by jbloom over 2 years ago - 1 comment

#125 - add reference to Yu et al citation

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

#124 - A regularization term that penalizes similarity between epitope escape profiles

Issue - State: closed - Opened by timcyu over 2 years ago - 28 comments

#122 - Add preprint link to docs

Pull Request - State: closed - Opened by timcyu over 2 years ago - 1 comment

#121 - add citations to pre-print

Issue - State: closed - Opened by jbloom over 2 years ago

#120 - Windows specific int comparison error

Issue - State: open - Opened by Caleb-Carr over 2 years ago - 1 comment

#119 - Update experimental design notebooks

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

#118 - fixes / improvements to mut escape plotting

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

#117 - change escape plots (version 2.0)

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

#116 - allow negative site numbers

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

#115 - `PolyclonalCollection` still works if just one model

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

#114 - fixing two silly typos

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

#113 - keep sites correctly sorted in `PolyclonalCollection` output

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

#112 - heatmaps never filter wildtype with slider stats

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

#111 - biochemically order amino-acids for heatmap plotting

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

#110 - enable non-sequential-integer reference site numbering

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

#109 - order amino-acid alphabets differently?

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

#108 - select mutation escape values by number of models in which they are seen

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

#107 - Fix `SettingWithCopyWarning` in heatmap plotting

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

#105 - fix `pandas` warning from `polyclonal.plot` heatmap

Issue - State: closed - Opened by jbloom over 2 years ago

#104 - docs give installation instructions for 1.0

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

#103 - reference site numbering

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

#102 - filter by number of models in `PolyclonalCollection` plots

Issue - State: closed - Opened by jbloom over 2 years ago

#101 - plot / compute average as median in addition to mean

Issue - State: closed - Opened by jbloom over 2 years ago

#100 - notebooks test and plot `PolyclonalAverage`

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

#99 - plot mut escape correlation heatmaps

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

#98 - implement `PolyclonalAverage`

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

#96 - generalize `PolyclonalCollection` and implement `PolyclonalBootstrap`

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

#95 - average across `Polyclonal` models

Issue - State: closed - Opened by jbloom over 2 years ago

#93 - Further generalize `mut_escape_heatmap`

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

#92 - generalize `mut_escape_heatmap`

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

#91 - add installation instructions from GitHub

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

#89 - regularize epitope activities

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

#88 - fix bug in parameter check in `Polyclonal`

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