Ecosyste.ms: Issues

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GitHub / dms-vep/dms-vep-pipeline-3 issues and pull requests

#115 - enable multiple summary plots

Pull Request - State: closed - Opened by jbloom 8 months ago

#114 - lint Jupyter notebooks with `ruff`

Pull Request - State: closed - Opened by jbloom 8 months ago

#113 - summary.csv filtering

Issue - State: closed - Opened by Bernadetadad 8 months ago - 2 comments

#112 - allow non-alphanumeric characters in summary keys

Issue - State: closed - Opened by Bernadetadad 8 months ago - 1 comment

#111 - lint Jupyter notebooks by fixing `ruff.toml`

Issue - State: closed - Opened by jbloom 8 months ago

#110 - enable generation of multiple distinctly configured summary plots

Issue - State: closed - Opened by jbloom 9 months ago - 1 comment

#107 - "minimum max" filter bug

Issue - State: open - Opened by Bernadetadad 9 months ago - 3 comments

#106 - fix `.gitignore` in test example

Pull Request - State: closed - Opened by jbloom 10 months ago

#105 - Add single nucleotide accessibility to heatmaps

Issue - State: open - Opened by Bernadetadad 10 months ago

#104 - gitignore wrong file name

Issue - State: closed - Opened by Bernadetadad 10 months ago

#103 - pipeline runs when `antibody_escape_config` is `null`

Pull Request - State: closed - Opened by jbloom 10 months ago

#102 - Pipeline not running without antibody escape

Issue - State: closed - Opened by arjunaditham 10 months ago - 8 comments

#101 - better error messages when problems with `barcode_runs`

Pull Request - State: closed - Opened by jbloom 10 months ago

#100 - snakemake issue with the latest environment update

Issue - State: closed - Opened by Bernadetadad 10 months ago - 2 comments

#99 - add `func_effect_diffs` rule

Pull Request - State: closed - Opened by jbloom 10 months ago

#98 - update environment

Pull Request - State: closed - Opened by jbloom 10 months ago

#97 - Add functional scores to multidms heatmaps

Issue - State: closed - Opened by Bernadetadad 10 months ago - 1 comment

#95 - Periodic Wildcard Error

Issue - State: closed - Opened by jbloom 11 months ago

#94 - constrain `{chart}` wildcard in `format_altair`

Pull Request - State: closed - Opened by jbloom 11 months ago

#93 - move model instantiation inside loop

Pull Request - State: closed - Opened by jgallowa07 11 months ago - 3 comments

#92 - `multidms` fitting bug in func_effect_shifts.ipynb

Issue - State: closed - Opened by jgallowa07 11 months ago - 3 comments

#91 - 86 1 multidms softplus clipping

Pull Request - State: open - Opened by jgallowa07 12 months ago - 2 comments

#90 - site highlighting broken in summary plots

Issue - State: closed - Opened by jbloom about 1 year ago - 2 comments

#89 - Fix bug in reporting pre-selection counts cutoff in `func_scores`

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

#88 - Fix bug in reporting pre-selection counts cutoff in `func_scores`

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

#87 - Issue with displaying cutoff in 'analyze_func_scores'

Issue - State: closed - Opened by bblarsen-sci about 1 year ago - 1 comment

#86 - Updating `multidms` fitting

Issue - State: open - Opened by jgallowa07 about 1 year ago - 11 comments

#84 - Fix bug introduced in `summary` when no antibodies in version 3.5.1

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

#83 - `summary` rule creates `per_antibody_escape.csv`

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

#82 - fix tooltips in columns with `.` in name

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

#80 - allow customization of x-axis in prob escape plots

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

#79 - filter noisy measurements with high standard deviations

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

#78 - enable filtering of measurements that are highly disparate among replicates

Issue - State: closed - Opened by jbloom about 1 year ago - 1 comment

#77 - Pipeline getting hung up near final steps

Issue - State: closed - Opened by bblarsen-sci about 1 year ago - 5 comments

#76 - added `baltic` to environment

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

#75 - update `dmslogo` to 0.7.0 to fix #74

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

#74 - Potential package version conflict with dmslogo?

Issue - State: closed - Opened by Caleb-Carr about 1 year ago - 2 comments

#73 - update `conda` env

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

#72 - Allow to invert concentration scale

Issue - State: closed - Opened by Bernadetadad about 1 year ago - 6 comments

#70 - `summary` plots allow fixed limits

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

#69 - add max_fixed to summary plots

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

#68 - Unknown javascript error in summary html plot

Issue - State: closed - Opened by Caleb-Carr about 1 year ago - 4 comments

#67 - Order antibodies in `summary` plots as ordered in config

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

#66 - make summary plots customizable for antibody order

Issue - State: closed - Opened by bblarsen-sci about 1 year ago - 1 comment

#65 - Fix bug when `barcode_counts` set to `null`

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

#64 - Issue setting `barcode_runs` to `null`

Issue - State: closed - Opened by WillHannon-MCB about 1 year ago - 1 comment
Labels: bug

#62 - Error in summary.ipynb when other_assays is empty

Issue - State: closed - Opened by Caleb-Carr about 1 year ago - 3 comments

#61 - Add `configure-dms-viz` to the pipeline

Issue - State: open - Opened by WillHannon-MCB about 1 year ago - 2 comments

#60 - give interpretable error if non-alphanumeric antibody names in `summary`

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

#59 - Fix bug so `summary` works even if no antibody escape data

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

#58 - problem with v3.4.1 summary HTML page not showing data

Issue - State: closed - Opened by bblarsen-sci about 1 year ago - 2 comments

#57 - Fix bug in site sorting in line plots in `summary.ipynb`

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

#56 - create summary across assays

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

#53 - fix axis label overlap on some site plots

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

#52 - do not display ICXX values by default

Issue - State: closed - Opened by jbloom over 1 year ago

#51 - fix bug introduced when adding `assays` in d39f3bcac2

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

#50 - generalize to allow arbitrary assays in `antibody_escape_config`

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

#49 - Do not show assays in the docs if no samples for that assay

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

#48 - display additional site numbers in tooltips

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

#47 - Allow alternative references

Issue - State: closed - Opened by Bernadetadad over 1 year ago - 3 comments

#46 - Plot same escape metric for replicates that is used for final average plot

Issue - State: closed - Opened by Caleb-Carr over 1 year ago - 2 comments

#45 - de-clutter HTML docs by arranging into subsections

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

#44 - update to `polyclonal` 6.7 to improve plotting

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

#43 - Bug in tooltips after applying functional selection filter

Issue - State: closed - Opened by Caleb-Carr over 1 year ago

#42 - Add `other_target_files` to make other files pipeline targets

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

#41 - de-clutter HTML docs

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

#40 - Escape colour scale

Issue - State: closed - Opened by Bernadetadad over 1 year ago - 2 comments

#38 - Fitting antibodies that don't fully neutralize

Issue - State: closed - Opened by Bernadetadad over 1 year ago - 1 comment

#37 - Add `min_filters` to `plot_hide_stats`

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

#36 - Constrain wildcards in `format_altair_html` to better enable custom rules

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

#35 - update to `polyclonal` 6.6 and improve plots

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

#34 - switch order of `df_to_merge`

Issue - State: closed - Opened by jbloom over 1 year ago

#33 - dump ordered YAML dicts, fixes bug from last commit

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

#32 - antibody_escape.smk bug or unclear issue with antibody selection input

Issue - State: closed - Opened by caelanradford over 1 year ago - 3 comments

#31 - generalize to plot mutation effects on receptor affinity

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

#30 - internal restructure so altair formatting common rule

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

#29 - Allowing strings for site numbering

Issue - State: closed - Opened by Bernadetadad over 1 year ago - 3 comments

#27 - Potential assertion bug in avg_func_effect_shifts.ipynb

Issue - State: closed - Opened by Caleb-Carr over 1 year ago

#26 - upgrade to `polyclonal` 6.5

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

#25 - by default interactive plots only show mutations in > half of replicates

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

#23 - add analysis of `func_effect_shifts` (becomes version 3.1.0)

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

#22 - allow underscores in antibody escape samples

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

#21 - Sample naming clarification

Issue - State: closed - Opened by Bernadetadad over 1 year ago - 3 comments

#20 - improve plotting in antibody escape notebooks

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

#19 - some discussion notes from Jesse re antibody selections

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

#16 - add plots of diversity to `analyze_variant_counts`

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