dms-vep dms-vep-pipeline-3 issues

dms-vep / dms-vep-pipeline-3

Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)

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issues

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update software and improve global epistasis convergence

#162 jbloom closed 3 days ago
0
pipeline is using old `altair` version

#161 jbloom opened 4 days ago
0
way to combine measurements from different parts of protein when averaging

#160 jbloom opened 6 days ago
0
alternative to GitHub to storing large results from pipeline?

#159 jbloom opened 6 days ago
3
Issue with multiDMS v0.3.3

#158 bblarsen-sci closed 3 days ago
6
add option to not show heatmaps in summary plots

#157 jbloom closed 1 week ago
0
Allow JSON in GitHub pages docs

#156 jbloom closed 4 weeks ago
0
download altair line plots separately

#155 Bernadetadad closed 1 week ago
3
feature request - improve escape count summary plots (low priority)

#154 bblarsen-sci opened 1 month ago
4
Update `snakemake`, `altair`, and `upsetplot` versions in `environment.yml`

#153 jbloom closed 1 month ago
0
151 remove defaults channel

#152 Caleb-Carr closed 1 month ago
0
defaults in environment yaml

#151 Caleb-Carr closed 1 month ago
3
update to `polyclonal 6.12`

#150 jbloom closed 2 months ago
0
Align zoom bar to line plot

#149 Bernadetadad closed 2 months ago
1
add `duplicate_fastq_R1` option

#148 jbloom closed 4 months ago
0
Allowing re-use of barcode run files in barcode_runs.csv

#147 arjunaditham closed 4 months ago
1
Is there a better way to display the polyclonal fitting based on different concentrations?

#146 bblarsen-sci closed 4 months ago
1
Update `multidms` to allow pandas update.

#145 jgallowa07 closed 5 months ago
1
we need to either update `multidms` immediately to fix serious bug, or stop using it

#144 jbloom closed 5 months ago
3
make `use_precomputed_barcode_counts` backward compatible

#143 jbloom closed 5 months ago
0
add option to use pre-computed barcode counts

#142 jbloom closed 5 months ago
0
create options to **not** require FASTQ input

#141 jbloom closed 5 months ago
1
Test on pull requests, deploy on pushes to main

#140 WillHannon-MCB closed 6 months ago
0
Fix issues with `Altair.vue`

#139 WillHannon-MCB closed 6 months ago
1
make correlation scatter plots in notebooks that avg replicates

#138 jbloom closed 6 months ago
0
Replicate correlation scatterplots plots

#137 Bernadetadad closed 6 months ago
1
Fix significant numbers on sliders

#136 bblarsen-sci closed 6 months ago
1
General improvements to the VitePress documentation

#135 WillHannon-MCB closed 6 months ago
0
Disable 'dark mode' in VitePress documentation

#134 WillHannon-MCB closed 6 months ago
0
make and save scatter plot in func effect diffs

#133 jbloom closed 6 months ago
0
Stochastic duplication of `Altair` plots on VitePress homepage

#132 WillHannon-MCB closed 6 months ago
3
more instructions for VitePress homepage

#131 jbloom closed 6 months ago
0
add Google Analytics instructions for VitePress page

#130 jbloom closed 6 months ago
0
what is relationship between `.vitepress/config.mjs` and `index.md` metadata for VitePress?

#129 jbloom closed 6 months ago
1
Upgrade GitHub actions to use Node 20.X

#128 WillHannon-MCB closed 6 months ago
0
VitePress deployment failure

#127 jbloom closed 6 months ago
3
more customization of summaries config

#126 jbloom closed 6 months ago
0
fix zooming of line plot in site summary

#125 jbloom closed 6 months ago
0
zooming in on summary plots no longer zooms on line plots

#124 jbloom closed 6 months ago
0
remove altair figure legends / titles

#123 jbloom closed 7 months ago
0
add mutation annotations

#122 jbloom closed 7 months ago
0
remove titles / legends from interactive figures in place of VitePress configuration

#121 jbloom closed 7 months ago
2
allow VitePress config to be omitted

#120 jbloom closed 7 months ago
0
structure annotations on heatmaps

#119 Bernadetadad closed 7 months ago
2
site phenotype tool

#118 Bernadetadad opened 7 months ago
10
Jesse edits to VitePress addition

#117 jbloom closed 7 months ago
0
Add documentation for creating a homepage with `VitePress`

#116 WillHannon-MCB closed 7 months ago
7
enable multiple summary plots

#115 jbloom closed 7 months ago
0
lint Jupyter notebooks with `ruff`

#114 jbloom closed 7 months ago
0
summary.csv filtering

#113 Bernadetadad closed 7 months ago
2