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Manage scanpy plots#23

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ralatsdc wants to merge 28 commits intoJCVenterInstitute:masterJCVenterInstitute/NSForest:masterfrom ralatsdc:ralatsdc/manage_sc_plotsralatsdc/NSForest:ralatsdc/manage_sc_plotsCopy head branch name to clipboard

+506-41

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Commits on Jul 24, 2024

• Prevent showing of the dendrogram

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  75928a7

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• Add script to run nsforest

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• Add shebang line

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• Add execute to all

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Commits on Sep 4, 2024

• Take a first pass at deconstructing NS-Forest script

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• Raise total counts substantially

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• Clean up arguments

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Commits on Sep 10, 2024

• Rename output files

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Commits on Sep 18, 2024

• Add header arg option to run_nsforest_on_file

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• Add header arg option to run_nsforest_on_file

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• Add arg to specify results_dirpath

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Commits on Sep 25, 2024

• Merge pull request #3 from ralatsdc/rl/deconstruct-nextflow-script

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• Merge remote-tracking branch 'upstream/master'

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Commits on Sep 26, 2024

• Make downsampling optional and not done by default

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Commits on Sep 27, 2024

• Merge pull request #4 from ralatsdc/rl/test_nsforest_module

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Commits on Sep 30, 2024

• Add preprocessing option, including use of cluster_list keyword argument

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• Add function to prefix file extensions

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• Add missing parenthesis

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• Fix import

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• Fix results path

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• Merge pull request #5 from ralatsdc/ralatsdc/add-preprocessing-option

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• Fix results directory path throughout

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• Move positional argument

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• Allow the cluster list to be input as a scalar

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Commits on Oct 1, 2024

• Add output file as key

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• Prevent use of empty dataframe

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Commits on Oct 2, 2024

• Merge pull request #6 from ralatsdc/ralatsdc/fix-result-directory-path

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Commits on Jan 8, 2025

• Save plots as SVGs, and remove some whitespace. Resisted blackening.

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