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Merge Daniel's developmental branch#224

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dzhu8 merged 238 commits intomainaristoteleo/spateo-release:mainfrom dzhu_devaristoteleo/spateo-release:dzhu_devCopy head branch name to clipboardFeb 7, 2024

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Commits

Commits on Mar 9, 2023

• Starting to add to spatial regression core

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Commits on Mar 15, 2023

• Moved generalized_lm and spatial_regression to temporary Deprecated folder

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Commits on Mar 23, 2023

• Moved more regression files to Deprecated

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Commits on Mar 25, 2023

• Add new databases, start building up new regression core

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Commits on Mar 27, 2023

• Add to distributions

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• Add more to distributions, remove references to binomial

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Commits on Mar 28, 2023

• Edit distributions

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• Adjust variable names in distributions

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• Update to distributions

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Commits on Mar 29, 2023

• Updates to regression

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Commits on Mar 30, 2023

• Update iwls

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Commits on Mar 31, 2023

• Code IWLS algorithm

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• Update to regression_utils

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Commits on Apr 1, 2023

• Start filling out the GWR class

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Commits on Apr 2, 2023

• Add preprocessing to new regression core

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• Add main executable for spatial regression

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Commits on Apr 3, 2023

• Add golden search for optimum bandwidth

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Commits on Apr 4, 2023

• More updates to spatial regression

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Commits on Apr 5, 2023

• Update to regression model

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• Adjust diagnostics pipeline for non-Gaussian models

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Commits on Apr 6, 2023

• Finished GWR core

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• More updates to spatial reg

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• Add main run file, other small updates

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Commits on Apr 8, 2023

• Update STGWR

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Commits on Apr 9, 2023

• Add GWRGRN, refactoring, add new databases

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• Update GRN model

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• Update GWR model

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Commits on Apr 10, 2023

• Add main run file

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• Minor updates

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Commits on Apr 11, 2023

• Bug fixing

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Commits on Apr 12, 2023

• Finished main multiscale procedure

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• Small update to multiscale core

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Commits on Apr 14, 2023

• Updates to design matrix setup

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Commits on Apr 15, 2023

• Updates to multiscale modules

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Commits on Apr 16, 2023

• Multiscale update

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Commits on Apr 17, 2023

• Bug testing

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Commits on Apr 18, 2023

• Added functionality for the case of cell-intrinsic modeling

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Commits on Apr 20, 2023

• Add subsampling functionality

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Commits on Apr 21, 2023

• Result of a lot of iteration

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• Updates to multiscale- fit on linear predictor

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Commits on Apr 22, 2023

• Update

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Commits on Apr 23, 2023

• Updates

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Commits on Apr 24, 2023

• Update to GLM multiscale

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• Small updates

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Commits on Apr 26, 2023

• Removed Hessian for now

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• Small update

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Commits on Apr 27, 2023

• Update to GRN model configuration

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Commits on Apr 28, 2023

• Small updates

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Commits on Apr 30, 2023

• Update to subsampling

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Commits on May 2, 2023

• Update GRN model

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Commits on May 3, 2023

• Preliminary GRN models do not work well- delete

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Commits on May 5, 2023

• Bug fixes

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• Refactor modeling package

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Commits on May 6, 2023

• Slight mods to utils

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Commits on May 8, 2023

• Update to setup

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Commits on May 10, 2023

• Updates

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• Bug fixes

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Commits on May 11, 2023

• Bug fixes

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• Modified regularization and preprocessing

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Commits on May 15, 2023

• Guided upstream target/predictor selection

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• Update X block setup

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Commits on May 16, 2023

• Add to upstream selection

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Commits on May 17, 2023

• Add to upstream selector class

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Commits on May 18, 2023

• Preparing for hurdle implementation

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• Update hurdle model

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Commits on May 19, 2023

• Added hurdle component + tweaking

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Commits on May 20, 2023

• Update subset

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Commits on May 21, 2023

• Modified statistical testing

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Commits on May 22, 2023

• Defined tools for arrow-drawing plots

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• Add plot functions for directional plots

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• Implement plotting for arrows

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Commits on May 23, 2023

• Fixed bug in significance testing

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Commits on May 24, 2023

• Tweaks to arrow plotting function

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• Minor fix to arrow drawing

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Commits on May 26, 2023

• Effect directions- compatibility with sparse matrices

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Commits on May 28, 2023

• Slight design tweaks

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• More conditions for bandwidth searching

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• More design matrix tweaks

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Commits on May 29, 2023

• Misc. minor changes

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Commits on May 31, 2023

• GAM helper functions

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Commits on Jun 2, 2023

• Spline fitting functions

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Commits on Jun 4, 2023

• Updates to GAM modeling

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Commits on Jun 5, 2023

• Statistical testing for GAM fitting

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Commits on Jun 6, 2023

• Downstream preprocessing

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Commits on Jun 10, 2023

• TMM normalization + polygon plotting

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• Bug fix

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Commits on Jun 12, 2023

• Add signaling DEG clustering, add Leiden clustering

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• Signaling DEG plotting

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• Small updates to signaling DEG plotting

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• Formatting for color label

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Commits on Jun 13, 2023

• Updates to normalize

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• Name updates

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• Typo fixes

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Commits on Jun 14, 2023

• Save design matrix

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• Small fix

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• Bug fix

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Commits on Jun 15, 2023

• Cell type coupling to downstream functions

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Commits on Jun 16, 2023

• Temporarily deprecated upstream feature selection

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Commits on Jun 18, 2023

• (I think?) complete downstream functionality, update run files and update upstream selection

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• Bug fixes

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Commits on Jun 20, 2023

• Generic update

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Commits on Jun 21, 2023

• Update docstrings

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• Update argparse

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• Update argparse

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Commits on Jun 22, 2023

• Update argparse

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• Misc. updates

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Commits on Jun 23, 2023

• Misc. updates

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Commits on Jun 24, 2023

• Refactor GAM core

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Commits on Jun 25, 2023

• Found/fixed major issue in normalization

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Commits on Jun 26, 2023

• Add updated human GRN- large file.

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• Refactor databases

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• Update databases again

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Commits on Jul 5, 2023

• Many misc. changes

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Commits on Jul 6, 2023

• Edits to smoothing

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• Update smooth function

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Commits on Jul 9, 2023

• Filtered cofactor and TF interaction databases

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Commits on Jul 10, 2023

• Add dimensionality reduction functions from Dynamo

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• Small updates

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Commits on Jul 12, 2023

• Reconfigured import statements, improved algorithm (I think)

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• Typo fix

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• Finishing touches?

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Commits on Jul 13, 2023

• Renamed outer CCI effects package

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Commits on Jul 14, 2023

• Adjust variable-scale model

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Commits on Jul 16, 2023

• SWR implementation tweaks

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• Small misc. changes

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Commits on Jul 17, 2023

• Jaccard-based adaptive bandwidth adjustment

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• Reverted back to slightly older version of algo

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Commits on Jul 19, 2023

• Framework adjustments!

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Commits on Jul 20, 2023

• More bandwidth-finding options

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• Typo fixes, adjustments to neighbor finding

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• Bug fix

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Commits on Jul 24, 2023

• Add to downstream analysis funcs

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• Misc. small fixes

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• Edits to downstream analysis functions

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Commits on Jul 25, 2023

• Begin definition of downstream effects model

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• Update downstream model

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Commits on Jul 27, 2023

• Sender deg downstream analysis

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Commits on Jul 28, 2023

• More downstream functions

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Commits on Jul 29, 2023

• Misc. changes

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• Misc. changes

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Commits on Aug 10, 2023

• Adjustment to upstream selection

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Commits on Aug 12, 2023

• Update upstream

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Commits on Aug 13, 2023

• Update selector

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Commits on Aug 14, 2023

• Edit downstream functions

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Commits on Aug 15, 2023

• Misc. changes

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Commits on Aug 16, 2023

• Fixes

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• Clean up, add visualization for downstream model

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Commits on Aug 17, 2023

• Edit downstream

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• Update downstream

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Commits on Aug 18, 2023

• Small updates to downstream

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Commits on Aug 19, 2023

• Mods to downstream

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Commits on Aug 21, 2023

• Re-included plot_connections

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Commits on Aug 23, 2023

• Interactions plot adjustments

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Commits on Aug 25, 2023

• Add multiplicity plot, adjust FC plot

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Commits on Sep 18, 2023

• Variant of highly variable genes that works on dense data

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Commits on Sep 22, 2023

• Downstream model update

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Commits on Sep 23, 2023

• Modify computation of pairwise distances

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Commits on Sep 25, 2023

• Update network construction

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• Update intercellular network

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• Update network plot

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Commits on Sep 26, 2023

• Customize network plotting

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Commits on Sep 27, 2023

• Many updates

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Commits on Oct 3, 2023

• Update README

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• Update intercellular networks

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Commits on Oct 5, 2023

• Update network and plotting function

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Commits on Oct 25, 2023

• Modify subsampling, add partial corr

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Commits on Oct 26, 2023

• Finish partial corr function

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• Add option for total counts-based subsetting

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Commits on Oct 27, 2023

• Bug fixes

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Commits on Oct 29, 2023

• Mouse db doesn't have pathway information

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Commits on Oct 31, 2023

• Update docstrings- for smoothing funcs

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Commits on Nov 1, 2023

• Edit order for Notch in DB

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Commits on Nov 4, 2023

• Misc fixes

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• Update to smoothing funcs

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Commits on Nov 7, 2023

• Updated Jaccard implementation

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Commits on Nov 9, 2023

• Final update to smoothing

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Commits on Nov 12, 2023

• Updates to model

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Commits on Nov 13, 2023

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