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fastTopics wrapper #151

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fastTopics wrapper #151

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Commits on Jan 14, 2021

  1. Working on FitTopicModel and fast_topics_demo example script.

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  2. Made a few small improvements to the fastTopics demo.

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  3. Filled out more of the roxygen2 docs for FitTopicModel.

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  4. Made several improvements to the roxygen2 docs for FitTopicModel, and… 

    … fixed the handling of the features (in particular, we avoid using VariableFeatures).
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Commits on Jan 15, 2021

  1. Improved fasttopics example; fixed PCA reduction key.

    @pcarbo
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  2. Revised the FitTopicModel roxygen2 docs.

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  3. Completed fast_topics_demo.R script.

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  4. First build of the fasttopics vignette.

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  5. More additions to the fasttopics vignette.

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  6. Some minor adjustments to the fasttopics vignette.

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  7. Made a few small revisions to the vignette.

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  8. Added fastTopics to README.

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  9. Added vignette title in README.

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  10. A couple of small edits to the fasttopics code.

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Commits on Jan 16, 2021

  1. Fixed PCA plot in fasttopics vignette.

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Commits on Jan 18, 2021

  1. Implemented helper functions prepare_counts_fasttopics and pca_from_l… 

    …oadings_fasttopics.
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  2. Implemented FitPoissonNMF.

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Commits on Jan 19, 2021

  1. Filled out roxygen2 docs for FitPoissonNMF.

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Commits on Feb 19, 2021

  1. Added notes from Alan.

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Commits on Feb 25, 2021

  1. Added notes from Gilad Green.

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Commits on Mar 3, 2021

  1. Added reduction.pca.name and reduction.pca.key arguments to fastTopic… 

    …s interface.
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  2. Added docs/fasttopics_files.

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Commits on Mar 4, 2021

  1. Updated verbose argument in FitTopicModel and FitPoissonNMF.

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Commits on Mar 15, 2023

  1. Merge remote-tracking branch 'upstream/master'.

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  2. Removed .DS_Store.

    @pcarbo
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  3. Added fastTopics to READMEs.

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  4. Added link to README.

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  5. Updated citations in fasttopics vignette.

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  6. Merge branch 'master' of github.com:stephenslab/seurat-wrappers.

    @pcarbo
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  7. Rebuilt the fasttopics vignettes.

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  8. Fixed the formatting of the citations in the fasttopics vignette.

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  9. Merge branch 'master' of github.com:stephenslab/seurat-wrappers.

    @pcarbo
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  10. A few small edits to the fasttopics vignette.

    @pcarbo
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  11. Rebuilt html for fasttopics vignette.

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Commits on Mar 16, 2023

  1. A few small revisions to the fasttopics vignette.

    @pcarbo
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  2. Merge branch 'master' of github.com:stephenslab/seurat-wrappers.

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  3. Rebuilt the fasttopics vignette html.

    @pcarbo
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  4. Small fix to the fasttopics rmd.

    @pcarbo
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  5. Added some text to the vignette explaining the structure plot.

    @pcarbo
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  6. Regenerated the markdown and html for fasttopics; the html is no long… 

    …er self contained.
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Commits on Mar 17, 2023

  1. Fixed a comment in the fasttopics vignette.

    @pcarbo
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  2. A few edits to the text in the fasttopics vignette.

    @pcarbo
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  3. Started implementation of PerformGoMDEAnalysis.

    @pcarbo
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  4. Updated roxygen2 for FitPoissonNMF and FitTopicModel.

    @pcarbo
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  5. Filled out most of the implementation for PerformGoMDEAnalysis.

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  6. Revised the misc slot for the dimreduc objects in the fasttopics func… 

    …tions.
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  7. Updated the html for the fasttopics vignette.

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Commits on Mar 18, 2023

  1. Added volcano plots to the fasttopics vignette.

    @pcarbo
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  2. Rebuilt fasttopics vignette.

    @pcarbo
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  3. A few fixes to the fasttopics rmd.

    @pcarbo
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Commits on Mar 20, 2023

  1. A few edits to the fasttopics vignette.

    @pcarbo
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  2. Merge branch 'master' of github.com:stephenslab/seurat-wrappers.

    @pcarbo
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  3. Small edit to the fasttopics vignette.

    @pcarbo
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  4. Revised the volcano plots and accompanying text in the fasttopics vig… 

    …nette.
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  5. Rebuilt the fasttopics md vignette.

    @pcarbo
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