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Dev ck #70

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Commits on May 22, 2020

  1. Merge pull request AllenInstitute#56 from AllenInstitute/master 

    merge master with dev_zy
    @yzizhen
    yzizhen committed May 22, 2020
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  2. More efficient DE gene calculation

    @yzizhen
    yzizhen committed May 22, 2020
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Commits on May 31, 2020

  1. Propagate the updates for de_genes

    @yzizhen
    yzizhen committed May 31, 2020
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Commits on Jun 3, 2020

  1. Propogate the differences in de.gene computation

    @yzizhen
    yzizhen committed Jun 3, 2020
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  2. Allow rd.dat and rd.dat.t

    @yzizhen
    yzizhen committed Jun 3, 2020
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  3. Change typo

    @yzizhen
    yzizhen committed Jun 3, 2020
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Commits on Jun 22, 2020

  1. Add elbow test for PCA

    @yzizhen
    yzizhen committed Jun 22, 2020
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Commits on Jun 26, 2020

  1. Fix name space issue

    @yzizhen
    yzizhen committed Jun 26, 2020
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Commits on Jul 9, 2020

  1. Restructure code

    @yzizhen
    yzizhen committed Jul 9, 2020
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Commits on Jul 10, 2020

  1. propagate the changes in de_genes functions

    @yzizhen
    yzizhen committed Jul 10, 2020
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  2. bug fix

    @yzizhen
    yzizhen committed Jul 10, 2020
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  3. fix typo

    @yzizhen
    yzizhen committed Jul 10, 2020
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Commits on Jul 11, 2020

  1. Bug fix

    @yzizhen
    yzizhen committed Jul 11, 2020
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Commits on Jul 17, 2020

  1. Fix typo

    @yzizhen
    yzizhen committed Jul 17, 2020
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  2. Add back the zscore method for determine the maximum number of PCs

    @yzizhen
    yzizhen committed Jul 17, 2020
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Commits on Jul 18, 2020

  1. Bug fix

    @yzizhen
    yzizhen committed Jul 18, 2020
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Commits on Aug 29, 2020

  1. Add package name to function call to reduce name conflict. Improve im… 

    …putation efficiency
    @yzizhen
    yzizhen committed Aug 29, 2020
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  2. fix typo

    @yzizhen
    yzizhen committed Aug 29, 2020
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Commits on Sep 30, 2020

  1. Add plotting function and more parallel processing

    @yzizhen
    yzizhen committed Sep 30, 2020
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Commits on Oct 1, 2020

  1. Updated plot_2d_umap_anno.

    @cvanvelt
    cvanvelt committed Oct 1, 2020
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  2. Update to plot_2d_umap_anno. Adding plotting options.

    @cvanvelt
    cvanvelt committed Oct 1, 2020
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  3. Merge pull request AllenInstitute#59 from AllenInstitute/feature/plot… 

    …_2d_umap_anno

Feature/plot 2d umap anno
    @yzizhen
    yzizhen committed Oct 1, 2020
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Commits on Oct 9, 2020

  1. change adjust_color function

    @yzizhen
    yzizhen committed Oct 9, 2020
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  2. Merge branch 'dev_zy' of https://github.com/AllenInstitute/scrattch.h… 

    …icat into dev_zy

Conflicts:
	R/reduceDimension_plot.R
    @yzizhen
    yzizhen committed Oct 9, 2020
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Commits on Dec 4, 2020

  1. add parallel mode for select_pos_markers

    @yzizhen
    yzizhen committed Dec 4, 2020
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Commits on Jan 26, 2021

  1. Fix namespace issue

    @yzizhen
    yzizhen committed Jan 26, 2021
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Commits on Feb 4, 2021

  1. Use loessFit from limma for loess fitting

    @yzizhen
    yzizhen committed Feb 4, 2021
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Commits on Feb 12, 2021

  1. Add merging step to each bootstrapping iteration in consensus cluster

    @yzizhen
    yzizhen committed Feb 12, 2021
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Commits on Feb 16, 2021

  1. Add imputation function implemented using Rcpp

    @yzizhen
    yzizhen committed Feb 16, 2021
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  2. Increase version number

    @yzizhen
    yzizhen committed Feb 16, 2021
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  3. Fix typo

    @yzizhen
    yzizhen committed Feb 16, 2021
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  4. Resolve namespace

    @yzizhen
    yzizhen committed Feb 16, 2021
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Commits on Feb 22, 2021

  1. Switch doParallel with doMC package for parallelization

    @yzizhen
    yzizhen committed Feb 22, 2021
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  2. Switch Rphenograph package

    @yzizhen
    yzizhen committed Feb 22, 2021
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Commits on Feb 24, 2021

  1. Bug fix with predict_knn

    @yzizhen
    yzizhen committed Feb 24, 2021
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  2. Bug fix with predict_knn

    @yzizhen
    yzizhen committed Feb 24, 2021
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  3. predict_knn bug fix

    @yzizhen
    yzizhen committed Feb 24, 2021
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  4. Remove obsolete functions

    @yzizhen
    yzizhen committed Feb 24, 2021
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  5. change NAMESPACE

    @yzizhen
    yzizhen committed Feb 24, 2021
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  6. Add RcppExport.R

    @yzizhen
    yzizhen committed Feb 24, 2021
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  7. Add RcppExport.cpp

    @yzizhen
    yzizhen committed Feb 24, 2021
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Commits on Mar 8, 2021

  1. Bug fix for impute_knn

    @yzizhen
    yzizhen committed Mar 8, 2021
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  2. Remove debugging comments

    @yzizhen
    yzizhen committed Mar 8, 2021
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  3. Simplify merging of small clusters during merging

    @yzizhen
    yzizhen committed Mar 8, 2021
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Commits on Mar 9, 2021

  1. Typo fix

    @yzizhen
    yzizhen committed Mar 9, 2021
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Commits on Mar 29, 2021

  1. Update patchseq script. Build building reference function

    @yzizhen
    yzizhen committed Mar 29, 2021
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Commits on Mar 30, 2021

  1. bug fix for harmonize function

    @yzizhen
    yzizhen committed Mar 30, 2021
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Commits on Apr 30, 2021

  1. bug fix for imputation

    @yzizhen
    yzizhen committed Apr 30, 2021
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Commits on May 4, 2021

  1. Bug fix for imputation

    @yzizhen
    yzizhen committed May 4, 2021
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  2. Remove unused function

    @yzizhen
    yzizhen committed May 4, 2021
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  3. Modify ImputeKnn arguments

    @yzizhen
    yzizhen committed May 4, 2021
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  4. Update RcppExport

    @yzizhen
    yzizhen committed May 4, 2021
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Commits on May 11, 2021

  1. control the number of cores to use based on the job size

    @yzizhen
    yzizhen committed May 11, 2021
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  2. re-implement predict_knn

    @yzizhen
    yzizhen committed May 11, 2021
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  3. increase version number

    @yzizhen
    yzizhen committed May 11, 2021
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  4. update predict_knn function

    @yzizhen
    yzizhen committed May 11, 2021
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Commits on May 18, 2021

  1. Update predict_knn function, and modify ComputeSNN function from Seur… 

    …at for jaccard distance computation
    @yzizhen
    yzizhen committed May 18, 2021
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  2. Remove debug message

    @yzizhen
    yzizhen committed May 18, 2021
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Commits on May 20, 2021

  1. Add l2norm function

    @yzizhen
    yzizhen committed May 20, 2021
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Commits on Jun 11, 2021

  1. Add Rcpp parallel function

    @y-gao
    y-gao committed Jun 11, 2021
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  2. Merge pull request AllenInstitute#63 from y-gao/dev_yg_test 

    Add Rcpp parallel function
    @yzizhen
    yzizhen committed Jun 11, 2021
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Commits on Jun 12, 2021

  1. Add get_cl_present and get_cl_sqr_means

    @y-gao
    y-gao committed Jun 12, 2021
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Commits on Jun 15, 2021

  1. Add get_cl_medians function

    @y-gao
    y-gao committed Jun 15, 2021
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  2. Merge pull request AllenInstitute#64 from y-gao/dev_yg_test 

    Add get_cl_present and get_cl_sqr_means
    @yzizhen
    yzizhen committed Jun 15, 2021
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Commits on Jun 16, 2021

  1. modify debug info

    @yzizhen
    yzizhen committed Jun 16, 2021
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  2. Link Rcpp file and unify indent

    @y-gao
    y-gao committed Jun 16, 2021
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Commits on Jun 17, 2021

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

    Link Rcpp file and unify indent
    @yzizhen
    yzizhen committed Jun 17, 2021
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Commits on Jun 23, 2021

  1. Modify plot_3d functions

    @yzizhen
    yzizhen committed Jun 23, 2021
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  2. Update reduceDimension_plot.R

    @yzizhen
    yzizhen committed Jun 23, 2021
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Commits on Jun 24, 2021

  1. Update 3d rglwidget plotting

    @cvanvelt
    cvanvelt committed Jun 24, 2021
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Commits on Jul 3, 2021

  1. Fix bug in rcpp_get_sqr_means

    @y-gao
    y-gao committed Jul 3, 2021
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  2. Merge pull request AllenInstitute#67 from y-gao/dev_yg_test 

    Fix bug in rcpp_get_sqr_means
    @yzizhen
    yzizhen committed Jul 3, 2021
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Commits on Jul 13, 2021

  1. Bug fix with merge_cl

    @yzizhen
    yzizhen committed Jul 13, 2021
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  2. Merge branch 'dev_zy' of https://github.com/AllenInstitute/scrattch.h… 

    …icat into dev_zy
    @yzizhen
    yzizhen committed Jul 13, 2021
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  3. Bug fix with harmonize function

    @yzizhen
    yzizhen committed Jul 13, 2021
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Commits on Jul 14, 2021

  1. change default distance matrix

    @yzizhen
    yzizhen committed Jul 14, 2021
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Commits on Jul 23, 2021

  1. to deal with missing marker genes in the data

    @leechangkyu
    leechangkyu committed Jul 23, 2021
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  2. to write out number of missing marker genes

    @leechangkyu
    leechangkyu committed Jul 23, 2021
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