Code

Version 2.1#261

Code

Merged

csangara merged 59 commits intomastersaeyslab/nichenetr:masterfrom develsaeyslab/nichenetr:develCopy head branch name to clipboardApr 25, 2024

+11,778-14,907

Commits

Commits on Aug 22, 2023

• add functions for preparing l-r heatmap

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• minor change to get_lfc_celltype

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• minor changes to vignettes (get_lfc_celltype)

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• new functions for drawing circos

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• update namespace

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Commits on Aug 24, 2023

• liana vignette

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• update liana vignette

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• update text

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Commits on Sep 6, 2023

• changes with unranked color scaling and ... args

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• add minmax scaling as argument

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• fix vignette

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Commits on Sep 7, 2023

• Merge branch 'master' into devel

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Commits on Sep 29, 2023

• calculate p-value

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• update gitignore

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• update seurat prioritization

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• rd file

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• changed directories

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Commits on Nov 13, 2023

• add line plot code

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• replace several packages with tidyverse instead

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Commits on Nov 15, 2023

• changes to mushroom and line plot for more customization

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• Merge branch 'master' into devel

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• minor change to get_lfc_celltype

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• line_plot doc

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Commits on Dec 20, 2023

• changed to solution that doesn't depend on R.utils

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Commits on Dec 21, 2023

• doc

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• add parallelization to permutation

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Commits on Jan 3, 2024

• add functions for nsga2r optimization

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• update man and namespace

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• update vignette

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Commits on Jan 24, 2024

• minor fix

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• update seurat vignettes

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• add figure

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• docs update

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• minor change to seurat vignette

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• ligand activity vignette

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• circos vignette

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• circos vignette

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Commits on Jan 26, 2024

• ligand signaling vignette update

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• moved images to specific folder, cleaned up directory

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• name chunks in rmarkdown

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• change to seurat object

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• readme

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Commits on Jan 29, 2024

• Merge branch 'master' into devel

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• update doc

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Commits on Jan 31, 2024

• update README

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• change draw_ to make_circos_plot for consistent naming

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• update assay_oi doc

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• major changes with prioritization

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• more tests for prioritization

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• Add separate legend option to make_circos_lr function

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• improved prioritization vignette

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• Update version to 2.1.0 in DESCRIPTION file

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Commits on Feb 6, 2024

• minor change

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• Update some functions to rename/add columns

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• fixed tests

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• Add dependencies

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Commits on Mar 25, 2024

• Merge branch 'master' into devel

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Commits on Apr 24, 2024

• add if statement for v5 object

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• FindAllMarkers still uses 'slot' even in v5

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