Update to TASBE 5#1

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jakebeal wants to merge 238 commits intoLivingComputingProject:masterfrom

Commits on May 18, 2017

improve explanation of colorpairfiles
jakebeal
authored

Commits on Jul 11, 2017

color model updated to use output directory settings
jakebeal
committed
Merge branch 'master' of https://github.com/TASBE/TASBEFlowAnalytics-Tutorial
jakebeal
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updated results files
jakebeal
committed

Commits on Sep 9, 2017

update CM to new gmdistribution constraints
jakebeal
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Commits on Sep 14, 2017

use update autogating
jakebeal
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one more update
jakebeal
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Commits on Sep 15, 2017

update test colormodel to 2.0 pre-release
jakebeal
committed

Commits on Sep 27, 2017

Commits on Sep 29, 2017

Add note about when to change AP number of Gaussian components
jakebeal
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Commits on Oct 14, 2017

correct typo
jakebeal
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Commits on Nov 15, 2017

Modified the datafile to include the new field added to ColorModel.
Lisa Tiberio
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Merge branch 'develop' into tutorial.ltiberio.bug86
Lisa Tiberio
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Commits on Nov 17, 2017

change FITC, MEFL to ERF where appropriate
jakebeal
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Merge branch 'master' into develop
jakebeal
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re-run color model to match revision
jakebeal
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Commits on Nov 20, 2017

Created a test wrapper for serialized output. Added the call to batch_template.
Lisa Tiberio
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Commits on Nov 29, 2017

Merge branch 'develop' into ltiberio.tutorial.issue95
Lisa Tiberio
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Unit test code.
Lisa Tiberio
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Commits on Dec 19, 2017

Moved this file into the TASBE code directory.
lisatiberio
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Commits on Jan 16, 2018

Commits on Jan 17, 2018

Merge commit '58a3955fb8431ec9b307b6750d36d9e65555a936' into develop
jakebeal
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Commits on Jan 18, 2018

Commits on Jan 21, 2018

Example of URCP-38-2K beads
jakebeal
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Merge branch 'develop'
jakebeal
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Commits on Jan 22, 2018

Commits on Jan 24, 2018

add comment showing how to use color models
jakebeal
authored

Commits on Jan 30, 2018

Merge pull request #25 from TASBE/develop
jakebeal
authored
add citation information
jakebeal
authored
update to better match OS
jakebeal
committed
Merge branch 'develop'
jakebeal
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Commits on Feb 11, 2018

Remove redundant CSV production
jakebeal
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update secondary bead channel example in template
jakebeal
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update use of serializeBatchOutput to reflect change to CSV naming, add CSVs
jakebeal
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adjust to reflect movement of bead_plot into TASBEConfig
jakebeal
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update secondary bead channel config
jakebeal
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don't need to plot path set to the default
jakebeal
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Commits on Feb 13, 2018

Commits on Feb 19, 2018

Fixing #138
jakebeal
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Commits on Feb 20, 2018

move rest of bead prefs into TASBEConfig
jakebeal
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updated colormodel
jakebeal
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Merge branch 'master' into develop
jakebeal
committed
Merge pull request #28 from TASBE/develop
jakebeal
authored

Commits on Mar 21, 2018

Commits on Mar 23, 2018

green shows up better than yellow
jakebeal
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Commits on Mar 28, 2018

Merge branch 'develop'
jakebeal
committed

Commits on Apr 6, 2018

Fix TASBEFlowAnalytics #200
jakebeal
committed

Commits on Jun 6, 2018

Updated tutorials 1-3
Cassandra Overney
committed

Commits on Jun 7, 2018

Made Requested Changes
Cassandra Overney
committed
Merge pull request #30 from TASBE/update-tutorials-1-3
jakebeal
authored

Commits on Jun 12, 2018

fixed issue 90 by adding a template that allows users to compare beadfiles
Cassandra Overney
committed

Commits on Jun 13, 2018

made display a bit more informative
jakebeal
committed
Merge pull request #32 from TASBE/coverney.issue90
jakebeal
authored
Updated README
coverney
authored
Updated README
coverney
authored

Commits on Jun 15, 2018

Edited batch template for issue 214
Cassandra Overney
committed

Commits on Jun 18, 2018

Merge pull request #34 from TASBE/coverney.issue214
jakebeal
authored

Commits on Jun 19, 2018

Merge pull request #33 from TASBE/coverney.updateREADME
jakebeal
authored
Edited plusminus template for issue 105
Cassandra Overney
committed

Commits on Jun 22, 2018

Issue 105
Cassandra Overney
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Commits on Jun 24, 2018

Commits on Jun 27, 2018

Added excel template to tutorial
Cassandra Overney
committed
Requested changes regarding issue 60
Cassandra Overney
committed
Merge pull request #36 from TASBE/coverney.issue60
jakebeal
authored

Commits on Jun 28, 2018

Added second version of template
Cassandra Overney
committed
Updated excel template
Cassandra Overney
committed

Commits on Jul 1, 2018

Commits on Jul 2, 2018

batch.csv is obsolete, replaced by automatic CSVs
jakebeal
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Renamed example_assay files
Cassandra Overney
committed
Merge branch 'master' into coverney.excel
coverney
authored
Made order to channel names match
Cassandra Overney
committed
Merge branch 'coverney.excel' of https://github.com/TASBE/TASBEFlowAnalytics-Tutorial into coverney.excel
Cassandra Overney
committed
Added batch_template using tutorial data
Cassandra Overney
committed

Commits on Jul 3, 2018

Merge pull request #38 from TASBE/coverney.excel
jakebeal
authored
Excel wrapper README file
Cassandra Overney
committed
Updated batch_template file
Cassandra Overney
committed
Formatting changes to ExcelREADME
coverney
authored
Updated Excel_README
coverney
authored
Updated one of the example templates
Cassandra Overney
committed
Merge branch 'coverney.excel' of https://github.com/TASBE/TASBEFlowAnalytics-Tutorial into coverney.excel
Cassandra Overney
committed

Commits on Jul 5, 2018

Updated batch_template spreadseet
Cassandra Overney
committed
Updated template Excel files
Cassandra Overney
committed

Commits on Jul 9, 2018

Typo in plusminus template!
Cassandra Overney
committed
Updated batch_template
Cassandra Overney
committed

Commits on Jul 10, 2018

Fixed typo in transfer curve template to work with new plot_bin_statistics function
Cassandra Overney
committed

Commits on Jul 12, 2018

Updated Excel batch_template
Cassandra Overney
committed

Commits on Jul 13, 2018

Updated batch_template spreadsheet
Cassandra Overney
committed

Commits on Jul 17, 2018

Update batch_template
Cassandra Overney
committed

Commits on Jul 20, 2018

Updated Excel README and batch_template
Cassandra Overney
committed
Updated Excel README
coverney
authored

Commits on Jul 22, 2018

Updated batch_template
Cassandra Overney
committed

Commits on Jul 23, 2018

Updated template in response to issue #306
Cassandra Overney
committed

Commits on Jul 24, 2018

Fixed issue #309, added example for point cloud filenames
Cassandra Overney
committed
Updated template to address issue #283
Cassandra Overney
committed
Formatting changes to template and updated Excel README
Cassandra Overney
committed

Commits on Jul 30, 2018

Updated batch template
Cassandra Overney
committed
Merge pull request #39 from TASBE/coverney.excel
jakebeal
authored

Commits on Aug 1, 2018

Updated optional settings
Cassandra Overney
committed
Merge pull request #40 from TASBE/coverney.excel
jakebeal
authored

Commits on Aug 2, 2018

Commits on Aug 3, 2018

Updated template
Cassandra Overney
committed

Commits on Aug 7, 2018

Updated batch template
Cassandra Overney
committed
Merge pull request #44 from TASBE/coverney.excel
jakebeal
authored

Commits on Aug 8, 2018

Updated batch template
Cassandra Overney
committed
Merge pull request #45 from TASBE/coverney.excel
jakebeal
authored

Commits on Aug 13, 2018

note how to do FSC/SSC
jakebeal
committed
Merge pull request #46 from TASBE/develop
jakebeal
authored

Commits on Aug 14, 2018

Updated template with multithreading features
Cassandra Overney
committed
Merge pull request #47 from TASBE/coverney.excel
jakebeal
authored
Updated Excel README with info on new features
Cassandra Overney
committed
Made requested changes to README
Cassandra Overney
committed
Merge pull request #48 from TASBE/coverney.excel
jakebeal
authored
Added string trim to VBA functions
Cassandra Overney
committed
Merge pull request #49 from TASBE/coverney.excel
jakebeal
authored

Commits on Aug 17, 2018

Merge pull request #50 from TASBE/develop
jakebeal
authored

Commits on Sep 9, 2018

Adding travis CI to tutorial
Cassandra Overney
committed
Added test functions for remaining tutorials, CM generation, and analysis
Cassandra Overney
committed
Modified directories to work with Travis CI
Cassandra Overney
committed

Commits on Sep 17, 2018

touch to try to trigger first build
jakebeal
authored

Commits on Sep 20, 2018

Adding matlab_compat and octave_compat folders to tutorial to get Travis CI working
Cassandra Overney
committed
Merge branch 'coverney.issue139' of https://github.com/TASBE/TASBEFlowAnalytics-Tutorial into coverney.issue139
Cassandra Overney
committed
Added makefile to tutorial for Travis CI
Cassandra Overney
committed
Added gmdistribution, library_code, tasbe_set_path functions for Travis CI
Cassandra Overney
committed
deleted tasbe_set_path function and instance for Travis CI
Cassandra Overney
committed
removing TASBEConfig instances in test functions for TravisCI
Cassandra Overney
committed
trying to find TASBEFlowAnalytics path from tutorial folder in TravisCI
Cassandra Overney
committed
trying to find path to TASBEFlowAnalytics in tutorial's TravisCI
Cassandra Overney
committed
trying to find TASBEFlowAnalytics in tutorial TravisCI
Cassandra Overney
committed
still trying to find path to TASBEFlowAnalytics
Cassandra Overney
committed
installing TASBEFlowAnalytics in tutorial .yml file for TravisCI
Cassandra Overney
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adding TASBEConfig test mode to tutorial TravisCI
Cassandra Overney
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setting TASBEConfig checkpoint to 'test'
Cassandra Overney
committed
testing to make sure TravisCI will fail
Cassandra Overney
committed

Commits on Sep 21, 2018

changing TravisCI back
Cassandra Overney
committed

Commits on Sep 26, 2018

Updated .travis.yml file
Cassandra Overney
committed
Update ReadMe
Cassandra Overney
authored
Merge pull request #52 from TASBE/coverney.issue139
jakebeal
authored

Commits on Sep 30, 2018

Merge pull request #53 from TASBE/develop
jakebeal
authored

Commits on Oct 10, 2018

extend template to including forward scatter calibration
jakebeal
committed
fix uM -> um
jakebeal
committed

Commits on Oct 11, 2018

Commits on Oct 19, 2018

Linked website to README
Cassandra Overney
authored
Merge pull request #56 from TASBE/coverney.README
jakebeal
authored

Commits on Nov 2, 2018

Update README.md
jakebeal
authored

Commits on Nov 14, 2018

Updated batch_template to add size beads feature
Cassandra Overney
committed
Merge pull request #57 from TASBE/coverney.issue357
jakebeal
authored

Commits on Dec 18, 2018

Merge pull request #58 from TASBE/develop
jakebeal
authored

Commits on Feb 26, 2019

Commits on Feb 27, 2019

Commits on Feb 28, 2019

Created the batch_template_csv file and tested it with the new CSVReaderHeader config
coverney
committed
added test for batch_template_csv
coverney
committed
temp change branch from master to develop
coverney
committed

Commits on Mar 3, 2019

uncommit plots
jakebeal
committed

Commits on Mar 5, 2019

Merge pull request #61 from TASBE/coverney.issue410
jakebeal
authored
Updated tutorial JSON Header
coverney
committed
Updated travis.yml to test tutorial
coverney
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Set TASBE branch in .yml back to develop
coverney
committed

Commits on Mar 12, 2019

Updated color model and header JSON file
coverney
committed
Updated color model .mat file using Octave
coverney
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Merge pull request #62 from TASBE/coverney.json
jakebeal
authored

Commits on Mar 26, 2019

Updated batch template
coverney
committed
Added datafile objects to bead comparison tutorial
coverney
committed

Commits on Apr 2, 2019

Fixed DataFiles in tutorial and got bead comparison to work
coverney
committed

Commits on Apr 3, 2019

Added DataFile objects to TASBE tutorials
coverney
committed

Commits on Apr 10, 2019

Updated batch template and incorporated csv read feature
coverney
committed

Commits on Apr 11, 2019

Commits on Apr 12, 2019

Commits on Apr 14, 2019

update GMMGating to not use excess 'plots' parameter
jakebeal
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AutogateParameters --> TASBEConfig
jakebeal
committed

Commits on Apr 15, 2019

finished adjusting for issue 429
jakebeal
committed
remove obsolete plot calls
jakebeal
committed
Merge pull request #66 from TASBE/fix/issue.429
jakebeal
authored
fix missing gate argument in comment
jakebeal
committed

Commits on Apr 16, 2019

Commits on May 6, 2019

fix errors in comments of color model template
jakebeal
committed

Commits on May 13, 2019

Updated Optional Settings tab in Excel Interface
coverney
committed

Commits on May 14, 2019

Merge pull request #68 from TASBE/coverney.updateInterface
jakebeal
authored

Commits on Jun 22, 2019

Commits on Jun 29, 2019

Commits on Jul 26, 2019

Commits on Sep 4, 2019

add ACS SynBio TASBE publication reference
jakebeal
authored

Commits on Sep 5, 2019

update travis to migrate from trusty to xenial configuration
jakebeal
authored

Commits on Sep 11, 2019

try to add ghostscript
jakebeal
committed
looks like pstoedit is needed too
jakebeal
committed
try turning off graphics output
jakebeal
committed
fix checkpointing so that graphics off continues to be respected during tests
jakebeal
committed
Merge pull request #72 from TASBE/trusty-to-xenial-migration
jakebeal
authored

Commits on Sep 18, 2019

Commits on Oct 2, 2019

Updated README
Cassandra Overney
authored
Merge pull request #74 from TASBE/coverney.issue481
jakebeal
authored
Added checkboxes to excel interface
coverney
committed

Commits on Oct 3, 2019

Merge pull request #75 from TASBE/coverney.issue471
jakebeal
authored

Commits on Dec 14, 2019

Added in AppleScript file
Cassandra Overney
committed
Created user guide for macOS users
coverney
committed
Merge branch 'coverney.issue292' of https://github.com/TASBE/TASBEFlowAnalytics-Tutorial into coverney.issue292
coverney
committed

Commits on Dec 15, 2019

Integrated Windows and macOS interfaces
coverney
committed

Commits on Dec 16, 2019

Merge pull request #76 from TASBE/coverney.issue292
jakebeal
authored

Commits on Dec 17, 2019

Commits on Feb 5, 2020

Added drop down menus in "Samples" sheet
coverney
committed

Commits on Feb 6, 2020

Merge pull request #79 from TASBE/coverney.issue297
jakebeal
authored

Commits on May 8, 2020

add bad bead file example for testing
jakebeal
committed

Commits on Jul 22, 2020

add link to iGEM tutorial
jakebeal
authored

Commits on Sep 11, 2020

very small FCS files for new test
jakebeal
committed

Commits on Sep 18, 2020

adding additional test files
Jake Beal
committed
color model for small test
Jake Beal
committed