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leechangkyu wants to merge 78 commits intoAllenInstitute:masterAllenInstitute/scrattch.hicat:masterfrom leechangkyu:devCKleechangkyu/scrattch.hicat:devCKCopy head branch name to clipboard

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Commits on May 22, 2020

• Merge pull request AllenInstitute#56 from AllenInstitute/master

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• More efficient DE gene calculation

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Commits on May 31, 2020

• Propagate the updates for de_genes

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Commits on Jun 3, 2020

• Propogate the differences in de.gene computation

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• Allow rd.dat and rd.dat.t

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• Change typo

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Commits on Jun 22, 2020

• Add elbow test for PCA

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Commits on Jun 26, 2020

• Fix name space issue

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Commits on Jul 9, 2020

• Restructure code

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Commits on Jul 10, 2020

• propagate the changes in de_genes functions

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• bug fix

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• fix typo

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Commits on Jul 11, 2020

• Bug fix

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Commits on Jul 17, 2020

• Fix typo

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• Add back the zscore method for determine the maximum number of PCs

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Commits on Jul 18, 2020

• Bug fix

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Commits on Aug 29, 2020

• Add package name to function call to reduce name conflict. Improve imputation efficiency

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• fix typo

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Commits on Sep 30, 2020

• Add plotting function and more parallel processing

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Commits on Oct 1, 2020

• Updated plot_2d_umap_anno.

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• Update to plot_2d_umap_anno. Adding plotting options.

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• Merge pull request AllenInstitute#59 from AllenInstitute/feature/plot_2d_umap_anno

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Commits on Oct 9, 2020

• change adjust_color function

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• Merge branch 'dev_zy' of https://github.com/AllenInstitute/scrattch.hicat into dev_zy

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Commits on Dec 4, 2020

• add parallel mode for select_pos_markers

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Commits on Jan 26, 2021

• Fix namespace issue

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Commits on Feb 4, 2021

• Use loessFit from limma for loess fitting

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Commits on Feb 12, 2021

• Add merging step to each bootstrapping iteration in consensus cluster

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Commits on Feb 16, 2021

• Add imputation function implemented using Rcpp

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• Increase version number

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• Fix typo

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• Resolve namespace

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Commits on Feb 22, 2021

• Switch doParallel with doMC package for parallelization

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• Switch Rphenograph package

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Commits on Feb 24, 2021

• Bug fix with predict_knn

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• Bug fix with predict_knn

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• predict_knn bug fix

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• Remove obsolete functions

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• change NAMESPACE

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• Add RcppExport.R

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• Add RcppExport.cpp

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Commits on Mar 8, 2021

• Bug fix for impute_knn

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• Remove debugging comments

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• Simplify merging of small clusters during merging

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Commits on Mar 9, 2021

• Typo fix

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Commits on Mar 29, 2021

• Update patchseq script. Build building reference function

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Commits on Mar 30, 2021

• bug fix for harmonize function

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Commits on Apr 30, 2021

• bug fix for imputation

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Commits on May 4, 2021

• Bug fix for imputation

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• Remove unused function

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• Modify ImputeKnn arguments

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• Update RcppExport

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Commits on May 11, 2021

• control the number of cores to use based on the job size

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• re-implement predict_knn

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• increase version number

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• update predict_knn function

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Commits on May 18, 2021

• Update predict_knn function, and modify ComputeSNN function from Seurat for jaccard distance computation

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• Remove debug message

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Commits on May 20, 2021

• Add l2norm function

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Commits on Jun 11, 2021

• Add Rcpp parallel function

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• Merge pull request AllenInstitute#63 from y-gao/dev_yg_test

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Commits on Jun 12, 2021

• Add get_cl_present and get_cl_sqr_means

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Commits on Jun 15, 2021

• Add get_cl_medians function

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• Merge pull request AllenInstitute#64 from y-gao/dev_yg_test

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Commits on Jun 16, 2021

• modify debug info

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• Link Rcpp file and unify indent

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Commits on Jun 17, 2021

• Merge pull request AllenInstitute#65 from y-gao/dev_yg_test

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Commits on Jun 23, 2021

• Modify plot_3d functions

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• Update reduceDimension_plot.R

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Commits on Jun 24, 2021

• Update 3d rglwidget plotting

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Commits on Jul 3, 2021

• Fix bug in rcpp_get_sqr_means

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• Merge pull request AllenInstitute#67 from y-gao/dev_yg_test

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Commits on Jul 13, 2021

• Bug fix with merge_cl

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• Merge branch 'dev_zy' of https://github.com/AllenInstitute/scrattch.hicat into dev_zy

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• Bug fix with harmonize function

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Commits on Jul 14, 2021

• change default distance matrix

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Commits on Jul 23, 2021

• to deal with missing marker genes in the data

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• to write out number of missing marker genes

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