BrentLab yeastdnnexplorer issues

BrentLab / yeastdnnexplorer

A development environment to explore implementations of deep neural networks for predicting the relationship between transcription factor and target genes using binding and perturbation data

https://brentlab.github.io/yeastdnnexplorer/

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adding `condition` to the valid promotersetsig filters

#112 cmatKhan closed 1 day ago
0
adding source_name to promotersetsig and updating the interface tutorial

#111 cmatKhan closed 4 days ago
1
add `aggregated` to promotersetsig valid params

#110 cmatKhan closed 5 days ago
0
basic shiny_app structure complete

#109 cmatKhan closed 6 days ago
0
delmiter not found with combined binding callingcards

#108 cmatKhan closed 1 week ago
0
fixing the csv sniffer auto detection of delimiters

#107 cmatKhan closed 1 week ago
1
add patsy to pyproject.toml

#106 cmatKhan closed 1 week ago
0
Add patsy

#105 cmatKhan closed 1 week ago
1
Processing data tutorial

#104 ejiawustl closed 1 week ago
2
Add effect/pvalue selectors to ExpressionAPI()

#103 cmatKhan closed 1 week ago
1
improve error handling of effect_colname and pvalue_colname

#102 cmatKhan opened 2 weeks ago
0
Add branch protection CI to prevent pulls directly to main

#101 cmatKhan closed 2 weeks ago
0
This is getting the dev branch rebased onto the main branch

#100 cmatKhan closed 2 weeks ago
1
Add expression col selectors

#99 cmatKhan closed 2 weeks ago
1
Add `use_cache` to AbstractRecordsAndFilesAPI(); add expression/pval selectors to ExpressionAPI()

#98 cmatKhan closed 2 weeks ago
2
add LRR/LRB correlation plots to rank response view in shiny app

#97 cmatKhan opened 3 weeks ago
0
Adding update to manualqc

#96 cmatKhan closed 1 month ago
0
7/23/24 TODOs

#95 cmatKhan opened 1 month ago
1
adding tutorial exploring relationship between perturbation response and enrichment effect

#94 ejiawustl closed 1 month ago
44
Endpoints that return tsv need to read files in as tsv

#93 cmatKhan opened 2 months ago
1
table data retrieved as gzip; addtiional columns now present from DB

#92 cmatKhan closed 2 months ago
0
updating the tutorial to show how to use the aggregated data

#91 cmatKhan closed 2 months ago
0
Database Interface

#90 cmatKhan closed 2 months ago
1
prepare_data needs to be adjusted to take data from the database API

#89 cmatKhan opened 2 months ago
0
Calculate variance explained

#88 ejiawustl closed 1 month ago
6
make sure that the perturbation adjustment based on TF binding can adjust the effect down

#87 cmatKhan opened 3 months ago
0
fixed adjustment function so its based on enrichment strength

#86 ejiawustl closed 3 months ago
0
adding new file for explanation

#85 cmatKhan closed 3 months ago
0
Use variance explained to compare models with different variance scales

#84 cmatKhan opened 3 months ago
1
perturbation effect adjustment needs to depend on binding effect, and it should adjust down if binding strength is low

#83 cmatKhan closed 3 months ago
2
Bump codecov/codecov-action from 3 to 4

#82 dependabot[bot] opened 4 months ago
0
remove gh-pages badge

#81 cmatKhan closed 2 months ago
0
removing docs gh-actions; adding note on how to build in index/readme

#80 cmatKhan closed 4 months ago
0
debugging gh-pages

#79 cmatKhan closed 4 months ago
0
debugging gh-pages github actions

#78 cmatKhan closed 4 months ago
0
deploy as 0.0.1

#77 cmatKhan closed 4 months ago
0
removing experiments from src dir; updating docs md and index files

#76 cmatKhan closed 4 months ago
0
Bump mkdocs-material from 9.5.7 to 9.5.20

#75 dependabot[bot] opened 4 months ago
0
Cleaning up notebooks

#74 BenMueller1 closed 4 months ago
0
Rewrite generate_in_silico_data.ipynb to match new methods we are using, also delete old unused mean adjustment function

#73 BenMueller1 closed 4 months ago
0
Bump mkdocstrings[python] from 0.24.0 to 0.25.0

#72 dependabot[bot] opened 4 months ago
0
Update pytest requirement from ^7.4.4 to ^8.2.0

#71 dependabot[bot] opened 4 months ago
0
Adding in files

#70 BenMueller1 closed 4 months ago
0
Bump mkdocs-material from 9.5.7 to 9.5.19

#69 dependabot[bot] closed 4 months ago
1
Fixing

#68 BenMueller1 closed 4 months ago
0
Finishing up!

#67 BenMueller1 closed 4 months ago
2
Bump griffe from 0.39.1 to 0.44.0

#66 dependabot[bot] opened 4 months ago
0
add error condition testing dimensions of default adjustment function binding data argument

#65 cmatKhan closed 4 months ago
1
Work over last few months of project

#64 BenMueller1 closed 4 months ago
0
Bump griffe from 0.39.1 to 0.43.0

#63 dependabot[bot] closed 4 months ago
1