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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
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