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Merge Daniel's developmental branch #223

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wants to merge 235 commits into from
Closed

Merge Daniel's developmental branch #223

wants to merge 235 commits into from

Commits on Mar 9, 2023

  1. Starting to add to spatial regression core 

    And many other changes, mainly renaming variables, etc.
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Commits on Mar 15, 2023

  1. Moved generalized_lm and spatial_regression to temporary Deprecated f… 

    …older

Need to adjust this code- currently runs sub-optimally
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Commits on Mar 23, 2023

  1. Moved more regression files to Deprecated

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Commits on Mar 25, 2023

  1. Add new databases, start building up new regression core

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Commits on Mar 27, 2023

  1. Add to distributions

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  2. Add more to distributions, remove references to binomial

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Commits on Mar 28, 2023

  1. Edit distributions

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  2. Adjust variable names in distributions

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  3. Update to distributions

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Commits on Mar 29, 2023

  1. Updates to regression

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Commits on Mar 30, 2023

  1. Update iwls

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Commits on Mar 31, 2023

  1. Code IWLS algorithm

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  2. Update to regression_utils

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Commits on Apr 1, 2023

  1. Start filling out the GWR class

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Commits on Apr 2, 2023

  1. Add preprocessing to new regression core

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  2. Add main executable for spatial regression

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Commits on Apr 3, 2023

  1. Add golden search for optimum bandwidth

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Commits on Apr 4, 2023

  1. More updates to spatial regression

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Commits on Apr 5, 2023

  1. Update to regression model

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  2. Adjust diagnostics pipeline for non-Gaussian models

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Commits on Apr 6, 2023

  1. Finished GWR core 

    Hopefully works well
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  2. More updates to spatial reg

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  3. Add main run file, other small updates 

    Note to self: change the bandwidth search range to reflect the different length scales over which secreted and membrane-bound signaling can occur. Can be simple for now, membrane-bound's max being either the distance to the 10th nearest neighbor or 10 um...and secreted's BW can be anything, I suppose.
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Commits on Apr 8, 2023

  1. Update STGWR

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Commits on Apr 9, 2023

  1. Add GWRGRN, refactoring, add new databases

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  2. Update GRN model

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  3. Update GWR model

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Commits on Apr 10, 2023

  1. Add main run file

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  2. Minor updates

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Commits on Apr 11, 2023

  1. Bug fixing

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Commits on Apr 12, 2023

  1. Finished main multiscale procedure

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  2. Small update to multiscale core

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Commits on Apr 14, 2023

  1. Updates to design matrix setup

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Commits on Apr 15, 2023

  1. Updates to multiscale modules

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Commits on Apr 16, 2023

  1. Multiscale update

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Commits on Apr 17, 2023

  1. Bug testing

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Commits on Apr 18, 2023

  1. Added functionality for the case of cell-intrinsic modeling 

    More to come- this is dreadfully slow for non-Gaussian regressions at anything in the 1000s for number of samples
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Commits on Apr 20, 2023

  1. Add subsampling functionality

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Commits on Apr 21, 2023

  1. Result of a lot of iteration

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  2. Updates to multiscale- fit on linear predictor

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Commits on Apr 22, 2023

  1. Update

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Commits on Apr 23, 2023

  1. Updates

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Commits on Apr 24, 2023

  1. Update to GLM multiscale 

    Not sure of the best way to do this...when fitting to the linear predictor, betas are WAY too large
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  2. Small updates

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Commits on Apr 26, 2023

  1. Removed Hessian for now

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  2. Small update

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Commits on Apr 27, 2023

  1. Update to GRN model configuration

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Commits on Apr 28, 2023

  1. Small updates

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Commits on Apr 30, 2023

  1. Update to subsampling

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Commits on May 2, 2023

  1. Update GRN model

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Commits on May 3, 2023

  1. Preliminary GRN models do not work well- delete

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Commits on May 5, 2023

  1. Bug fixes

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  2. Refactor modeling package

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Commits on May 6, 2023

  1. Slight mods to utils

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Commits on May 8, 2023

  1. Update to setup

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Commits on May 10, 2023

  1. Updates

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  2. Bug fixes

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Commits on May 11, 2023

  1. Bug fixes

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  2. Modified regularization and preprocessing

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Commits on May 15, 2023

  1. Guided upstream target/predictor selection

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  2. Update X block setup

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Commits on May 16, 2023

  1. Add to upstream selection

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Commits on May 17, 2023

  1. Add to upstream selector class

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Commits on May 18, 2023

  1. Preparing for hurdle implementation

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  2. Update hurdle model

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Commits on May 19, 2023

  1. Added hurdle component + tweaking

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Commits on May 20, 2023

  1. Update subset

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Commits on May 21, 2023

  1. Modified statistical testing

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Commits on May 22, 2023

  1. Defined tools for arrow-drawing plots

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  2. Add plot functions for directional plots

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  3. Implement plotting for arrows 

    Untested so far
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Commits on May 23, 2023

  1. Fixed bug in significance testing

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Commits on May 24, 2023

  1. Tweaks to arrow plotting function

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  2. Minor fix to arrow drawing

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Commits on May 26, 2023

  1. Effect directions- compatibility with sparse matrices

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Commits on May 28, 2023

  1. Slight design tweaks

    @dzhu8
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  2. More conditions for bandwidth searching

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  3. More design matrix tweaks

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Commits on May 29, 2023

  1. Misc. minor changes

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Commits on May 31, 2023

  1. GAM helper functions

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Commits on Jun 2, 2023

  1. Spline fitting functions

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Commits on Jun 4, 2023

  1. Updates to GAM modeling

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Commits on Jun 5, 2023

  1. Statistical testing for GAM fitting

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Commits on Jun 6, 2023

  1. Downstream preprocessing

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Commits on Jun 10, 2023

  1. TMM normalization + polygon plotting

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  2. Bug fix

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Commits on Jun 12, 2023

  1. Add signaling DEG clustering, add Leiden clustering 

    Also removed some of the old clustering utils
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  2. Signaling DEG plotting

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  3. Small updates to signaling DEG plotting

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  4. Formatting for color label

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Commits on Jun 13, 2023

  1. Updates to normalize

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  2. Name updates

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  3. Typo fixes

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Commits on Jun 14, 2023

  1. Save design matrix

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  2. Small fix

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  3. Bug fix

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Commits on Jun 15, 2023

  1. Cell type coupling to downstream functions

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Commits on Jun 16, 2023

  1. Temporarily deprecated upstream feature selection 

    Will benchmark this with an alternative to decide which implementation to use- will do the same w/ the signaling DEG detection in the downstream module
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Commits on Jun 18, 2023

  1. (I think?) complete downstream functionality, update run files and up… 

    …date upstream selection
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  2. Bug fixes

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Commits on Jun 20, 2023

  1. Generic update

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Commits on Jun 21, 2023

  1. Update docstrings

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  2. Update argparse

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  3. Update argparse

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Commits on Jun 22, 2023

  1. Update argparse

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  2. Misc. updates

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Commits on Jun 23, 2023

  1. Misc. updates 

    Self-reminder to finish editing the GAM functions
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Commits on Jun 24, 2023

  1. Refactor GAM core

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Commits on Jun 25, 2023

  1. Found/fixed major issue in normalization

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    dzhu8 committed Jun 25, 2023
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Commits on Jun 26, 2023

  1. Add updated human GRN- large file.

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    dzhu8 committed Jun 26, 2023
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  2. Refactor databases

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    dzhu8 committed Jun 26, 2023
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  3. Update databases again 

    Noticed a few features that are not known to act as TFs but which are included as TFs- fixed this.

Also going to redo the upstream & downstream association testing
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    dzhu8 committed Jun 26, 2023
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Commits on Jul 5, 2023

  1. Many misc. changes

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    dzhu8 committed Jul 5, 2023
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Commits on Jul 6, 2023

  1. Edits to smoothing

    @dzhu8
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  2. Update smooth function 

    Stupid update took forever...
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    dzhu8 committed Jul 6, 2023
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Commits on Jul 9, 2023

  1. Filtered cofactor and TF interaction databases

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    dzhu8 committed Jul 9, 2023
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Commits on Jul 10, 2023

  1. Add dimensionality reduction functions from Dynamo

    @dzhu8
    dzhu8 committed Jul 10, 2023
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  2. Small updates

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    dzhu8 committed Jul 10, 2023
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Commits on Jul 12, 2023

  1. Reconfigured import statements, improved algorithm (I think)

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    dzhu8 committed Jul 12, 2023
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  2. Typo fix

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    dzhu8 committed Jul 12, 2023
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  3. Finishing touches?

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    dzhu8 committed Jul 12, 2023
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Commits on Jul 13, 2023

  1. Renamed outer CCI effects package

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Commits on Jul 14, 2023

  1. Adjust variable-scale model 

    Untested
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Commits on Jul 16, 2023

  1. SWR implementation tweaks 

    Incredibly improved performance!
    @dzhu8
    dzhu8 committed Jul 16, 2023
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  2. Small misc. changes

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    dzhu8 committed Jul 16, 2023
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Commits on Jul 17, 2023

  1. Jaccard-based adaptive bandwidth adjustment

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  2. Reverted back to slightly older version of algo 

    Better performance- also set a default value for lambda b/c it improves performance a lot
    @dzhu8
    dzhu8 committed Jul 17, 2023
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Commits on Jul 19, 2023

  1. Framework adjustments!

    @dzhu8
    dzhu8 committed Jul 19, 2023
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Commits on Jul 20, 2023

  1. More bandwidth-finding options

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  2. Typo fixes, adjustments to neighbor finding

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  3. Bug fix

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    dzhu8 committed Jul 20, 2023
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Commits on Jul 24, 2023

  1. Add to downstream analysis funcs

    @dzhu8
    dzhu8 committed Jul 24, 2023
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  2. Misc. small fixes

    @dzhu8
    dzhu8 committed Jul 24, 2023
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  3. Edits to downstream analysis functions

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    dzhu8 committed Jul 24, 2023
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Commits on Jul 25, 2023

  1. Begin definition of downstream effects model

    @dzhu8
    dzhu8 committed Jul 25, 2023
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  2. Update downstream model

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    dzhu8 committed Jul 25, 2023
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Commits on Jul 27, 2023

  1. Sender deg downstream analysis

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    dzhu8 committed Jul 27, 2023
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Commits on Jul 28, 2023

  1. More downstream functions

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Commits on Jul 29, 2023

  1. Misc. changes

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  2. Misc. changes

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Commits on Aug 10, 2023

  1. Adjustment to upstream selection

    @dzhu8
    dzhu8 committed Aug 10, 2023
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Commits on Aug 12, 2023

  1. Update upstream

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    dzhu8 committed Aug 12, 2023
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Commits on Aug 13, 2023

  1. Update selector

    @dzhu8
    dzhu8 committed Aug 13, 2023
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Commits on Aug 14, 2023

  1. Edit downstream functions

    @dzhu8
    dzhu8 committed Aug 14, 2023
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Commits on Aug 15, 2023

  1. Misc. changes

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    dzhu8 committed Aug 15, 2023
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Commits on Aug 16, 2023

  1. Fixes

    @dzhu8
    dzhu8 committed Aug 16, 2023
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  2. Clean up, add visualization for downstream model

    @dzhu8
    dzhu8 committed Aug 16, 2023
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Commits on Aug 17, 2023

  1. Edit downstream

    @dzhu8
    dzhu8 committed Aug 17, 2023
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  2. Update downstream

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    dzhu8 committed Aug 17, 2023
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Commits on Aug 18, 2023

  1. Small updates to downstream

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    dzhu8 committed Aug 18, 2023
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Commits on Aug 19, 2023

  1. Mods to downstream

    @dzhu8
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Commits on Aug 21, 2023

  1. Re-included plot_connections

    @dzhu8
    dzhu8 committed Aug 21, 2023
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Commits on Aug 23, 2023

  1. Interactions plot adjustments

    @dzhu8
    dzhu8 committed Aug 23, 2023
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Commits on Aug 25, 2023

  1. Add multiplicity plot, adjust FC plot

    @dzhu8
    dzhu8 committed Aug 25, 2023
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Commits on Sep 18, 2023

  1. Variant of highly variable genes that works on dense data

    @dzhu8
    dzhu8 committed Sep 18, 2023
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Commits on Sep 22, 2023

  1. Downstream model update 

    Start adding intercellular network vis
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    dzhu8 committed Sep 22, 2023
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Commits on Sep 23, 2023

  1. Modify computation of pairwise distances 

    And other changes
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Commits on Sep 25, 2023

  1. Update network construction

    @dzhu8
    dzhu8 committed Sep 25, 2023
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  2. Update intercellular network

    @dzhu8
    dzhu8 committed Sep 25, 2023
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  3. Update network plot

    @dzhu8
    dzhu8 committed Sep 25, 2023
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Commits on Sep 26, 2023

  1. Customize network plotting

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    dzhu8 committed Sep 26, 2023
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Commits on Sep 27, 2023

  1. Many updates 

    Updates to databases, downstream, main CCI module, networks
    @dzhu8
    dzhu8 committed Sep 27, 2023
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Commits on Oct 3, 2023

  1. Update README

    @dzhu8
    dzhu8 committed Oct 3, 2023
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  2. Update intercellular networks

    @dzhu8
    dzhu8 committed Oct 3, 2023
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Commits on Oct 5, 2023

  1. Update network and plotting function

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    dzhu8 committed Oct 5, 2023
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Commits on Oct 25, 2023

  1. Modify subsampling, add partial corr 

    Also pre-commit updates?
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    dzhu8 committed Oct 25, 2023
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Commits on Oct 26, 2023

  1. Finish partial corr function

    @dzhu8
    dzhu8 committed Oct 26, 2023
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  2. Add option for total counts-based subsetting

    @dzhu8
    dzhu8 committed Oct 26, 2023
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Commits on Oct 27, 2023

  1. Bug fixes

    @dzhu8
    dzhu8 committed Oct 27, 2023
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Commits on Oct 29, 2023

  1. Mouse db doesn't have pathway information

    @dzhu8
    dzhu8 committed Oct 29, 2023
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Commits on Oct 31, 2023

  1. Update docstrings- for smoothing funcs

    @dzhu8
    dzhu8 committed Oct 31, 2023
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Commits on Nov 1, 2023

  1. Edit order for Notch in DB

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    dzhu8 committed Nov 1, 2023
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Commits on Nov 4, 2023

  1. Misc fixes

    @dzhu8
    dzhu8 committed Nov 4, 2023
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  2. Update to smoothing funcs

    @dzhu8
    dzhu8 committed Nov 4, 2023
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Commits on Nov 7, 2023

  1. Updated Jaccard implementation

    @dzhu8
    dzhu8 committed Nov 7, 2023
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Commits on Nov 9, 2023

  1. Final update to smoothing

    @dzhu8
    dzhu8 committed Nov 9, 2023
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Commits on Nov 12, 2023

  1. Updates to model

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Commits on Nov 13, 2023

  1. Modify downstream funcs to look over only the true pos & true neg

    @dzhu8
    dzhu8 committed Nov 13, 2023
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  2. Database update

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    dzhu8 committed Nov 13, 2023
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Commits on Nov 14, 2023

  1. Remove MPI integration for now 

    Also update databases
    @dzhu8
    dzhu8 committed Nov 14, 2023
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  2. Updates

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    dzhu8 committed Nov 14, 2023
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Commits on Nov 19, 2023

  1. Modifications to downstream, main model

    @dzhu8
    dzhu8 committed Nov 19, 2023
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Commits on Nov 20, 2023

  1. Removed some parts of downstream module

    @dzhu8
    dzhu8 committed Nov 20, 2023
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Commits on Nov 21, 2023

  1. Modify LR databases

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    dzhu8 committed Nov 21, 2023
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Commits on Nov 27, 2023

  1. Update downstream functions

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    dzhu8 committed Nov 27, 2023
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Commits on Nov 30, 2023

  1. Mods + additions + removals- many new downstream functionalities

    @dzhu8
    dzhu8 committed Nov 30, 2023
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  2. Update downstream plotting

    @dzhu8
    dzhu8 committed Nov 30, 2023
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Commits on Dec 1, 2023

  1. Update to downstream

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    dzhu8 committed Dec 1, 2023
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Commits on Dec 3, 2023

  1. Update downstream functions 

    Also moved smoothing
    @dzhu8
    dzhu8 committed Dec 3, 2023
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  2. Moved adata filtering func

    @dzhu8
    dzhu8 committed Dec 3, 2023
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  3. Misc. updates

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Commits on Dec 4, 2023

  1. Downstream function update

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Commits on Dec 6, 2023

  1. Updates to downstream

    @dzhu8
    dzhu8 committed Dec 6, 2023
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  2. Update downstream

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    dzhu8 committed Dec 6, 2023
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Commits on Dec 7, 2023

  1. Update downstream

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  2. Update downstream

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    dzhu8 committed Dec 7, 2023
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Commits on Dec 11, 2023

  1. Minor update

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    dzhu8 committed Dec 11, 2023
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Commits on Dec 12, 2023

  1. Database update

    @dzhu8
    dzhu8 committed Dec 12, 2023
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Commits on Dec 16, 2023

  1. Add custom axis functions

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    dzhu8 committed Dec 16, 2023
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Commits on Dec 18, 2023

  1. Update downstream

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Commits on Dec 20, 2023

  1. Updates to plotting & downstream

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Commits on Dec 22, 2023

  1. Update downstream

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    dzhu8 committed Dec 22, 2023
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Commits on Dec 23, 2023

  1. Update downstream

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Commits on Dec 29, 2023

  1. Add 3D direction plotting code

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    dzhu8 committed Dec 29, 2023
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Commits on Dec 30, 2023

  1. Update 3D vector field plotting

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Commits on Dec 31, 2023

  1. Add gene expression heatmap functionality to downstream

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    dzhu8 committed Dec 31, 2023
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Commits on Jan 3, 2024

  1. Update 3D CCI plotting

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    dzhu8 committed Jan 3, 2024
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Commits on Jan 6, 2024

  1. Misc. changes

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    dzhu8 committed Jan 6, 2024
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  2. Merge branch 'main' into dzhu_dev

    @dzhu8
    dzhu8 committed Jan 6, 2024
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Commits on Jan 7, 2024

  1. Fix some errors 

    Includes deleting Deprecated folder
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  2. Merge branch 'main' into dzhu_dev

    @dzhu8
    dzhu8 committed Jan 7, 2024
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Commits on Jan 9, 2024

  1. Change to modeling framework 

    Remove feature masking
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Commits on Jan 10, 2024

  1. Small mods to modeling

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Commits on Jan 12, 2024

  1. Delete testing folder

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    dzhu8 committed Jan 12, 2024
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  2. Add adjustText to requirements

    @dzhu8
    dzhu8 committed Jan 12, 2024
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  3. Add psutil to installs

    @dzhu8
    dzhu8 committed Jan 12, 2024
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  4. Delete tests folder

    @dzhu8
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Commits on Jan 14, 2024

  1. Merge branch 'main' into dzhu_dev

    @dzhu8
    dzhu8 committed Jan 14, 2024
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Commits on Jan 16, 2024

  1. Misc. updates

    @dzhu8
    dzhu8 committed Jan 16, 2024
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  2. Adjustment to CCI modeling

    @dzhu8
    dzhu8 committed Jan 16, 2024
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Commits on Jan 21, 2024

  1. Updated downstream class

    @dzhu8
    dzhu8 committed Jan 21, 2024
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  2. Merge branch 'main' into dzhu_dev

    @dzhu8
    dzhu8 committed Jan 21, 2024
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Commits on Jan 22, 2024

  1. Update downstream

    @dzhu8
    dzhu8 committed Jan 22, 2024
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Commits on Jan 24, 2024

  1. Update downstream

    @dzhu8
    dzhu8 committed Jan 24, 2024
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Commits on Jan 26, 2024

  1. Update downstream

    @dzhu8
    dzhu8 committed Jan 26, 2024
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  2. Update lr_db_mouse.csv

    @dzhu8
    dzhu8 committed Jan 26, 2024
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Commits on Jan 27, 2024

  1. Update plotting functions

    @dzhu8
    dzhu8 committed Jan 27, 2024
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Commits on Jan 28, 2024

  1. Update model setup

    @dzhu8
    dzhu8 committed Jan 28, 2024
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  2. Small updates to plotting functions

    @dzhu8
    dzhu8 committed Jan 28, 2024
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Commits on Jan 31, 2024

  1. Add axolotl, Drosophila, zebrafish L:R lists again

    @dzhu8
    dzhu8 committed Jan 31, 2024
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  2. Merge branch 'main' into dzhu_dev

    @dzhu8
    dzhu8 committed Jan 31, 2024
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  3. Update main modeling core

    @dzhu8
    dzhu8 committed Jan 31, 2024
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Commits on Feb 1, 2024

  1. Merge branch 'main' into dzhu_dev

    @dzhu8
    dzhu8 committed Feb 1, 2024
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  2. Add tests folder back

    @dzhu8
    dzhu8 committed Feb 1, 2024
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  3. Update formatting for certain files

    @dzhu8
    dzhu8 committed Feb 1, 2024
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