1. celda
  2. DESCRIPTION
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:19:55
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DESCRIPTION
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 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.14.0
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+Version: 1.15.0
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:19:55
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DESCRIPTION
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 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.13.0
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+Version: 1.14.0
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
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Updated Matrix conversion calls to be compatible with Matrix v1.4-2

Joshua D. Campbell authored on 22/10/2022 02:00:54
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DESCRIPTION
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@@ -29,8 +29,8 @@ Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
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 LinkingTo: Rcpp, RcppEigen
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 License: MIT + file LICENSE
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 Encoding: UTF-8
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-LazyData: false
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-RoxygenNote: 7.1.2
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+LazyData: true
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+RoxygenNote: 7.2.1
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 BugReports: https://github.com/campbio/celda/issues
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 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian, ImmunoOncology, DataImport
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 NeedsCompilation: yes
Browse code

Updates to version number and NEWS

Joshua D. Campbell authored on 22/10/2022 00:50:46
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DESCRIPTION
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 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.12.0
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+Version: 1.13.0
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
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@@ -29,8 +29,8 @@ Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
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 LinkingTo: Rcpp, RcppEigen
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 License: MIT + file LICENSE
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 Encoding: UTF-8
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-LazyData: true
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+LazyData: false
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 RoxygenNote: 7.1.2
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 BugReports: https://github.com/campbio/celda/issues
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-biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian
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+biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian, ImmunoOncology, DataImport
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 NeedsCompilation: yes
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Version bump and update docs for BioC 3.15

Joshua D. Campbell authored on 30/04/2022 20:00:25
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DESCRIPTION
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 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.13.0
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+Version: 1.12.0
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:55:58
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DESCRIPTION
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 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.12.0
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+Version: 1.13.0
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:55:58
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DESCRIPTION
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 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.11.1
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+Version: 1.12.0
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
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Remove install commands in vignettes. Version bump

Joshua D. Campbell authored on 13/04/2022 19:55:44
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DESCRIPTION
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 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.11.0
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+Version: 1.11.1
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
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Merge remote-tracking branch 'bioc/master' into devel

Joshua D. Campbell authored on 29/03/2022 15:54:06
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Browse code

Moved Matrix and SingleCellExperiment to Depends to make sure these are loaded when using celda

Joshua D. Campbell authored on 25/03/2022 20:25:48
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DESCRIPTION
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@@ -14,15 +14,15 @@ Description: Celda is a suite of Bayesian hierarchical models for
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     Bayesian method to computationally estimate and remove RNA contamination in
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     individual cells without empty droplet information. A variety of scRNA-seq
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     data visualization functions is also included.
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-Depends: R (>= 4.0)
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+Depends: R (>= 4.0), SingleCellExperiment, Matrix
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 VignetteBuilder: knitr
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 Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
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         grDevices, graphics, matrixStats, doParallel, digest, methods,
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         reshape2, S4Vectors, data.table,
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         Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment,
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         MCMCprecision, ggrepel, Rtsne, withr,
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-        scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
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-        DelayedArray, stringr, Matrix, ComplexHeatmap, multipanelfigure,
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+        scater (>= 1.14.4), scran, dbscan,
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+        DelayedArray, stringr, ComplexHeatmap, multipanelfigure,
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         circlize
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 Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
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         BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:52:02
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DESCRIPTION
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 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.10.0
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+Version: 1.11.0
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 16:52:02
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DESCRIPTION
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 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.9.3
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+Version: 1.10.0
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
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Updated version, docs, nav bar, and NEWS

Joshua D. Campbell authored on 04/10/2021 16:44:28
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DESCRIPTION
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 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.9.2
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+Version: 1.9.3
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
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Style check

Yuan authored on 01/10/2021 15:27:46
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DESCRIPTION
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@@ -30,7 +30,7 @@ LinkingTo: Rcpp, RcppEigen
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 License: MIT + file LICENSE
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 Encoding: UTF-8
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 LazyData: true
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-RoxygenNote: 7.1.1
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+RoxygenNote: 7.1.2
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 BugReports: https://github.com/campbio/celda/issues
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 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian
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 NeedsCompilation: yes
Browse code

Moved author order in DESCRIPTION

Joshua D. Campbell authored on 20/09/2021 18:25:26
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DESCRIPTION
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@@ -3,11 +3,10 @@ Title: CEllular Latent Dirichlet Allocation
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 Version: 1.9.2
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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-    person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
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-    person("Yusuke", "Koga", email="ykoga07@bu.edu", role = c("aut")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
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-    person("Eric", "Reed", email="reeder@bu.edu", role = c("aut")),
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-    person("Zhe", "Wang", email="zhe@bu.edu", role = c("aut")))
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+    person("Zhe", "Wang", email="zhe@bu.edu", role = c("aut")),
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+    person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
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+    person("Yusuke", "Koga", email="ykoga07@bu.edu", role = c("aut")))
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 Description: Celda is a suite of Bayesian hierarchical models for
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     clustering single-cell RNA-sequencing (scRNA-seq) data. It is able to
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     perform "bi-clustering" and simultaneously cluster genes into gene modules
Browse code

Added back in necessary 'suggests' packages

Joshua D. Campbell authored on 17/09/2021 01:57:33
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DESCRIPTION
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@@ -26,7 +26,7 @@ Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
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         DelayedArray, stringr, Matrix, ComplexHeatmap, multipanelfigure,
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         circlize
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 Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
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-        BiocManager, BiocStyle, TENxPBMCData
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+        BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData
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 LinkingTo: Rcpp, RcppEigen
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 License: MIT + file LICENSE
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 Encoding: UTF-8
Browse code

Removed extra packages from the suggests of DESCRIPTION

Joshua D. Campbell authored on 12/09/2021 19:41:23
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DESCRIPTION
History View file @ 6127451e
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@@ -26,7 +26,7 @@ Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
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         DelayedArray, stringr, Matrix, ComplexHeatmap, multipanelfigure,
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         circlize
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 Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
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-        BiocManager, BiocStyle, M3DExampleData, TENxPBMCData, singleCellTK
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+        BiocManager, BiocStyle, TENxPBMCData
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 LinkingTo: Rcpp, RcppEigen
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 License: MIT + file LICENSE
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 Encoding: UTF-8
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minor tweaks to pkgdown docs

Joshua D. Campbell authored on 19/07/2021 17:40:48
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DESCRIPTION
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@@ -1,6 +1,6 @@
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 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.9.1
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+Version: 1.9.2
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
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version bump

zhewa authored on 28/05/2021 01:57:23
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DESCRIPTION
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1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.9.0
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+Version: 1.9.1
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:43:46
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DESCRIPTION
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@@ -1,6 +1,6 @@
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 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.8.0
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+Version: 1.9.0
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 16:43:46
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DESCRIPTION
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@@ -1,6 +1,6 @@
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 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.7.14
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+Version: 1.8.0
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

show empty gene in moduleHeatmap

zhewa authored on 17/05/2021 20:24:10
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DESCRIPTION
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@@ -1,6 +1,6 @@
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 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.7.13
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+Version: 1.7.14
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

version bump

zhewa authored on 13/05/2021 03:06:57
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DESCRIPTION
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1 1 
 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.7.12
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+Version: 1.7.13
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
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add displayName to featureModuleTable. Remove stringi

zhewa authored on 11/05/2021 15:10:13
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DESCRIPTION
History View file @ 3a9bde76
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@@ -20,7 +20,7 @@ VignetteBuilder: knitr
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 Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
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         grDevices, graphics, matrixStats, doParallel, digest, methods,
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         reshape2, S4Vectors, data.table,
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-        Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment,
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+        Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment,
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         MCMCprecision, ggrepel, Rtsne, withr,
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         scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
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         DelayedArray, stringr, Matrix, ComplexHeatmap, multipanelfigure,
Browse code

version bump

zhewa authored on 11/05/2021 13:43:13
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.7.11
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+Version: 1.7.12
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
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fix perplexity altExpName bug

zhewa authored on 10/05/2021 20:32:23
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.7.10
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+Version: 1.7.11
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
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add displayName to plotCeldaViolin. Fix bug. Version bump

zhewa authored on 10/05/2021 15:27:26
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.7.9
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+Version: 1.7.10
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

version bump

zhewa authored on 08/05/2021 19:58:39
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.7.8
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+Version: 1.7.9
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

add singleCellTK to suggests. update .gitignore

zhewa authored on 03/05/2021 13:29:26
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DESCRIPTION
History View file @ 09862e20
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@@ -26,7 +26,7 @@ Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
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         DelayedArray, stringr, Matrix, ComplexHeatmap, multipanelfigure,
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         circlize
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 Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
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-        BiocManager, BiocStyle, M3DExampleData, TENxPBMCData
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+        BiocManager, BiocStyle, M3DExampleData, TENxPBMCData, singleCellTK
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 LinkingTo: Rcpp, RcppEigen
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 License: MIT + file LICENSE
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 Encoding: UTF-8
Browse code

fix errors. Use \donttest. Version bump.

zhewa authored on 02/05/2021 18:48:49
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DESCRIPTION
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@@ -1,6 +1,6 @@
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 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.7.7
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+Version: 1.7.8
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

replace setReplaceMethod. Remove findMarkersTree, getDecisions

zhewa authored on 20/04/2021 14:16:59
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DESCRIPTION
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@@ -21,9 +21,9 @@ Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
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         grDevices, graphics, matrixStats, doParallel, digest, methods,
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         reshape2, S4Vectors, data.table,
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         Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment,
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-        MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro,
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-        pROC, scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
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-        DelayedArray, Seurat, stringr, Matrix, ComplexHeatmap, multipanelfigure,
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+        MCMCprecision, ggrepel, Rtsne, withr,
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+        scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
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+        DelayedArray, stringr, Matrix, ComplexHeatmap, multipanelfigure,
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         circlize
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 Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
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         BiocManager, BiocStyle, M3DExampleData, TENxPBMCData
Browse code

fix check notes

zhewa authored on 05/04/2021 20:54:09
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.7.6
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+Version: 1.7.7
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

version bump

Joshua D. Campbell authored on 05/04/2021 02:23:45
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.7.5
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+Version: 1.7.6
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

Removed differentialExpression related functions as these are now in the singleCellTK

Joshua D. Campbell authored on 22/03/2021 17:27:20
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DESCRIPTION
History View file @ 06243313
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@@ -19,7 +19,7 @@ Depends: R (>= 4.0)
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 VignetteBuilder: knitr
20 20 
 Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
21 21 
         grDevices, graphics, matrixStats, doParallel, digest, methods,
22 
-        reshape2, MAST, S4Vectors, data.table,
22 
+        reshape2, S4Vectors, data.table,
23 23 
         Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment,
24 24 
         MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro,
25 25 
         pROC, scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
Browse code

fix altExp bug, version bump

zhewa authored on 17/03/2021 18:48:54
Showing 1 changed files
DESCRIPTION
History View file @ ae78c402
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.7.4
3 
+Version: 1.7.5
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

update version to 1.7.4

Yuan authored on 10/03/2021 02:33:26
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DESCRIPTION
History View file @ f45bd1e7
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.7.3
3 
+Version: 1.7.4
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

version bump

zhewa authored on 09/11/2020 18:20:42
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DESCRIPTION
History View file @ e3f9537d
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.7.2
3 
+Version: 1.7.3
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

update Description

zhewa authored on 09/11/2020 18:12:40
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DESCRIPTION
History View file @ 81a12af2
... ... 
@@ -8,8 +8,14 @@ Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
8 8 
     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
9 9 
     person("Eric", "Reed", email="reeder@bu.edu", role = c("aut")),
10 10 
     person("Zhe", "Wang", email="zhe@bu.edu", role = c("aut")))
11 
-Description: Utilizing Bayesian hierarchical models to analyze single-cell genomic data.
12 
-Depends: R (>= 3.6)
11 
+Description: Celda is a suite of Bayesian hierarchical models for
12 
+    clustering single-cell RNA-sequencing (scRNA-seq) data. It is able to
13 
+    perform "bi-clustering" and simultaneously cluster genes into gene modules
14 
+    and cells into cell subpopulations. It also contains DecontX, a novel
15 
+    Bayesian method to computationally estimate and remove RNA contamination in
16 
+    individual cells without empty droplet information. A variety of scRNA-seq
17 
+    data visualization functions is also included.
18 
+Depends: R (>= 4.0)
13 19 
 VignetteBuilder: knitr
14 20 
 Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
15 21 
         grDevices, graphics, matrixStats, doParallel, digest, methods,
Browse code

version bump

zhewa authored on 08/11/2020 23:34:51
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DESCRIPTION
History View file @ 86d02738
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.7.1
3 
+Version: 1.7.2
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

remove Author, Maintainer, and Packaged fields

zhewa authored on 27/10/2020 17:38:54
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DESCRIPTION
History View file @ ba1e7692
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.7.0
3 
+Version: 1.7.1
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
... ... 
@@ -29,11 +29,3 @@ RoxygenNote: 7.1.1
29 29 
 BugReports: https://github.com/campbio/celda/issues
30 30 
 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian
31 31 
 NeedsCompilation: yes
32 
-Packaged: 2020-04-02 18:47:49 UTC; josh
33 
-Author: Joshua Campbell [aut, cre],
34 
-  Sean Corbett [aut],
35 
-  Yusuke Koga [aut],
36 
-  Shiyi Yang [aut],
37 
-  Eric Reed [aut],
38 
-  Zhe Wang [aut]
39 
-Maintainer: Joshua Campbell <camp@bu.edu>
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 15:46:07
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DESCRIPTION
History View file @ d1b0d082
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.6.0
3 
+Version: 1.7.0
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 15:46:07
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DESCRIPTION
History View file @ 7daa5e96
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.5.12
3 
+Version: 1.6.0
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

fix no visible binding for global variable note

zhewa authored on 21/10/2020 18:06:56
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DESCRIPTION
History View file @ 4c965367
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.5.11
3 
+Version: 1.5.12
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

fix doc warning file link in package does not exist and so has been treated as a topic

zhewa authored on 16/10/2020 21:36:32
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DESCRIPTION
History View file @ 82cc7a6a
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.5.10
3 
+Version: 1.5.11
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

version bump

zhewa authored on 15/10/2020 19:19:43
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DESCRIPTION
History View file @ 5548205e
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.5.9
3 
+Version: 1.5.10
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

fix doc, version bump

zhewa authored on 13/10/2020 19:34:43
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DESCRIPTION
History View file @ 7028c654
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.5.8
3 
+Version: 1.5.9
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

fix bioc check doc warning. Fix vignette

zhewa authored on 13/10/2020 18:47:29
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DESCRIPTION
History View file @ c6f36d75
... ... 
@@ -24,7 +24,7 @@ Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
24 24 
 LinkingTo: Rcpp, RcppEigen
25 25 
 License: MIT + file LICENSE
26 26 
 Encoding: UTF-8
27 
-LazyData: false
27 
+LazyData: true
28 28 
 RoxygenNote: 7.1.1
29 29 
 BugReports: https://github.com/campbio/celda/issues
30 30 
 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian
Browse code

fix import circlize

zhewa authored on 13/10/2020 01:53:15
Showing 1 changed files
DESCRIPTION
History View file @ 187f1b86
... ... 
@@ -17,8 +17,9 @@ Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
17 17 
         Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment,
18 18 
         MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro,
19 19 
         pROC, scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
20 
-        DelayedArray, Seurat, stringr, Matrix, ComplexHeatmap, multipanelfigure
21 
-Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, circlize
20 
+        DelayedArray, Seurat, stringr, Matrix, ComplexHeatmap, multipanelfigure,
21 
+        circlize
22 
+Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
22 23 
         BiocManager, BiocStyle, M3DExampleData, TENxPBMCData
23 24 
 LinkingTo: Rcpp, RcppEigen
24 25 
 License: MIT + file LICENSE
Browse code

fix doc, add import circlize

zhewa authored on 13/10/2020 01:52:03
Showing 1 changed files
DESCRIPTION
History View file @ 909e0208
... ... 
@@ -18,7 +18,7 @@ Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
18 18 
         MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro,
19 19 
         pROC, scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
20 20 
         DelayedArray, Seurat, stringr, Matrix, ComplexHeatmap, multipanelfigure
21 
-Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
21 
+Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, circlize
22 22 
         BiocManager, BiocStyle, M3DExampleData, TENxPBMCData
23 23 
 LinkingTo: Rcpp, RcppEigen
24 24 
 License: MIT + file LICENSE
Browse code

remove import gridExtra

zhewa authored on 13/10/2020 00:16:17
Showing 1 changed files
DESCRIPTION
History View file @ 0852212a
... ... 
@@ -12,8 +12,8 @@ Description: Utilizing Bayesian hierarchical models to analyze single-cell genom
12 12 
 Depends: R (>= 3.6)
13 13 
 VignetteBuilder: knitr
14 14 
 Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
15 
-        grDevices, graphics, matrixStats, doParallel, digest,
16 
-        gridExtra, methods, reshape2, MAST, S4Vectors, data.table,
15 
+        grDevices, graphics, matrixStats, doParallel, digest, methods,
16 
+        reshape2, MAST, S4Vectors, data.table,
17 17 
         Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment,
18 18 
         MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro,
19 19 
         pROC, scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
Browse code

update celdatosce, celda.rmd

zhewa authored on 10/10/2020 17:01:35
Showing 1 changed files
DESCRIPTION
History View file @ 53bd7c8d
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.5.7
3 
+Version: 1.5.8
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

fix version

zhewa authored on 09/10/2020 18:17:58
Showing 1 changed files
DESCRIPTION
History View file @ d8a63492
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.5.6
3 
+Version: 1.5.7
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

fix version

zhewa authored on 09/10/2020 18:02:56
Showing 1 changed files
DESCRIPTION
History View file @ 6cd2ab83
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.5.7
3 
+Version: 1.5.6
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

Merge branch 'sce' of github.com:zhewa/celda

zhewa authored on 09/10/2020 13:58:36
Showing 0 changed files
Browse code

add addons to .travis.yml to fix magick error on TRAVIS CI

zhewa authored on 30/09/2020 02:14:11
Showing 1 changed files
DESCRIPTION
History View file @ 5675c7e3
... ... 
@@ -36,10 +36,3 @@ Author: Joshua Campbell [aut, cre],
36 36 
   Eric Reed [aut],
37 37 
   Zhe Wang [aut]
38 38 
 Maintainer: Joshua Campbell <camp@bu.edu>
39 
-
40 
-addons:
41 
-  apt:
42 
-    sources:
43 
-    - sourceline: 'ppa:opencpu/imagemagick'
44 
-    packages:
45 
-    - libmagick++-dev
Browse code

add addons to DESCRIPTION to fix magick error on TRAVIS

zhewa authored on 29/09/2020 23:46:38
Showing 1 changed files
DESCRIPTION
History View file @ 6c0367d5
... ... 
@@ -36,3 +36,10 @@ Author: Joshua Campbell [aut, cre],
36 36 
   Eric Reed [aut],
37 37 
   Zhe Wang [aut]
38 38 
 Maintainer: Joshua Campbell <camp@bu.edu>
39 
+
40 
+addons:
41 
+  apt:
42 
+    sources:
43 
+    - sourceline: 'ppa:opencpu/imagemagick'
44 
+    packages:
45 
+    - libmagick++-dev
Browse code

add import multipanelfigure

zhewa authored on 29/09/2020 23:11:26
Showing 1 changed files
DESCRIPTION
History View file @ 2622563c
... ... 
@@ -17,7 +17,7 @@ Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
17 17 
         Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment,
18 18 
         MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro,
19 19 
         pROC, scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
20 
-        DelayedArray, Seurat, stringr, Matrix, ComplexHeatmap
20 
+        DelayedArray, Seurat, stringr, Matrix, ComplexHeatmap, multipanelfigure
21 21 
 Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
22 22 
         BiocManager, BiocStyle, M3DExampleData, TENxPBMCData
23 23 
 LinkingTo: Rcpp, RcppEigen
Browse code

multiple moduleHeatmap on same page. remove blank page

zhewa authored on 16/09/2020 15:50:01
Showing 1 changed files
DESCRIPTION
History View file @ 1d563e1f
... ... 
@@ -17,14 +17,14 @@ Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
17 17 
         Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment,
18 18 
         MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro,
19 19 
         pROC, scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
20 
-        DelayedArray, Seurat, stringr, Matrix
20 
+        DelayedArray, Seurat, stringr, Matrix, ComplexHeatmap
21 21 
 Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
22 22 
         BiocManager, BiocStyle, M3DExampleData, TENxPBMCData
23 23 
 LinkingTo: Rcpp, RcppEigen
24 24 
 License: MIT + file LICENSE
25 25 
 Encoding: UTF-8
26 26 
 LazyData: true
27 
-RoxygenNote: 7.1.0
27 
+RoxygenNote: 7.1.1
28 28 
 BugReports: https://github.com/campbio/celda/issues
29 29 
 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian
30 30 
 NeedsCompilation: yes
Browse code

fix lints

zhewa authored on 19/08/2020 01:33:33
Showing 1 changed files
DESCRIPTION
History View file @ fe2e65ed
... ... 
@@ -24,7 +24,7 @@ LinkingTo: Rcpp, RcppEigen
24 24 
 License: MIT + file LICENSE
25 25 
 Encoding: UTF-8
26 26 
 LazyData: false
27 
-RoxygenNote: 7.1.0
27 
+RoxygenNote: 7.1.1
28 28 
 BugReports: https://github.com/campbio/celda/issues
29 29 
 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian
30 30 
 NeedsCompilation: yes
Browse code

update doc

zhewa authored on 01/08/2020 11:59:44
Showing 1 changed files
DESCRIPTION
History View file @ 453f9bdb
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.5.6
3 
+Version: 1.5.7
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

Merge branch 'RELEASE_3_11' of github.com:zhewa/celda

zhewa authored on 07/06/2020 11:55:44
Showing 0 changed files
Browse code

pass initialDims in celdaTsneG

zhewa authored on 07/06/2020 11:53:15
Showing 1 changed files
DESCRIPTION
History View file @ 2d8577ac
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.4.5
3 
+Version: 1.4.6
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

fix travis errors

zhewa authored on 24/05/2020 08:51:11
Showing 1 changed files
DESCRIPTION
History View file @ 720dcf7c
... ... 
@@ -23,7 +23,7 @@ Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
23 23 
 LinkingTo: Rcpp, RcppEigen
24 24 
 License: MIT + file LICENSE
25 25 
 Encoding: UTF-8
26 
-LazyData: false
26 
+LazyData: true
27 27 
 RoxygenNote: 7.1.0
28 28 
 BugReports: https://github.com/campbio/celda/issues
29 29 
 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian
Browse code

use reducedDim for DR results, update examples

zhewa authored on 24/05/2020 08:14:12
Showing 1 changed files
DESCRIPTION
History View file @ f8826e1e
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.5.5
3 
+Version: 1.5.6
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

Merge branch 'RELEASE_3_11' of github.com:zhewa/celda

zhewa authored on 10/05/2020 06:47:08
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Browse code

version bump

zhewa authored on 10/05/2020 05:34:28
Showing 1 changed files
DESCRIPTION
History View file @ df5c4bfe
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.4.4
3 
+Version: 1.4.5
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

version bump

zhewa authored on 08/05/2020 06:25:05
Showing 1 changed files
DESCRIPTION
History View file @ 4e566baf
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.5.3
3 
+Version: 1.5.4
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

fix celda_G tsne UMAP dim reduction bug

zhewa authored on 08/05/2020 06:20:40
Showing 1 changed files
DESCRIPTION
History View file @ 3dd62ee6
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.4.3
3 
+Version: 1.4.4
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

version bump

zhewa authored on 01/05/2020 12:13:22
Showing 1 changed files
DESCRIPTION
History View file @ e44160a1
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.4.3
3 
+Version: 1.5.3
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

version bump

zhewa authored on 01/05/2020 12:11:11
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.4.2
3 
+Version: 1.4.3
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

version bump

zhewa authored on 01/05/2020 02:45:36
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.4.1
3 
+Version: 1.4.2
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
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version bump

zhewa authored on 29/04/2020 07:03:16
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.4.0
3 
+Version: 1.4.1
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
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bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 19:27:09
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.3.9
3 
+Version: 1.4.0
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
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version bump

zhewa authored on 21/04/2020 03:22:45
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DESCRIPTION
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.3.8
3 
+Version: 1.3.9
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

version 1.3.8 to observe Bioc convention

zhewa authored on 07/04/2020 06:17:37
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DESCRIPTION
History View file @ 486c95ba
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.4.0
3 
+Version: 1.3.8
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
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Finalized DecontX expression violin plot function and vignette.

Joshua D. Campbell authored on 06/04/2020 04:17:58
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DESCRIPTION
History View file @ 51477d47
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.3.6
3 
+Version: 1.4.0
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
... ... 
@@ -8,7 +8,7 @@ Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
8 8 
     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
9 9 
     person("Eric", "Reed", email="reeder@bu.edu", role = c("aut")),
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     person("Zhe", "Wang", email="zhe@bu.edu", role = c("aut")))
11 
-Description: celda is a Bayesian hierarchical model that can co-cluster features and cells in single cell sequencing data.
11 
+Description: Utilizing Bayesian hierarchical models to analyze single-cell genomic data.
12 12 
 Depends: R (>= 3.6)
13 13 
 VignetteBuilder: knitr
14 14 
 Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
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merge

Joshua D. Campbell authored on 03/04/2020 04:11:30
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Coverted DecontX C code to use RcppEigen instead of RcppArmadillo as it was faster and didn't prodcue warnings when checking

Joshua D. Campbell authored on 02/04/2020 20:56:09
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DESCRIPTION
History View file @ d671d202
... ... 
@@ -9,65 +9,30 @@ Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
9 9 
     person("Eric", "Reed", email="reeder@bu.edu", role = c("aut")),
10 10 
     person("Zhe", "Wang", email="zhe@bu.edu", role = c("aut")))
11 11 
 Description: celda is a Bayesian hierarchical model that can co-cluster features and cells in single cell sequencing data.
12 
-Depends:
13 
-    R (>= 3.6)
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+Depends: R (>= 3.6)
14 13 
 VignetteBuilder: knitr
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-Imports:
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-    plyr,
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-    foreach,
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-    ggplot2,
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-    RColorBrewer,
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-    grid,
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-    scales,
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-    gtable,
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-    grDevices,
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-    graphics,
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-    matrixStats,
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-    doParallel,
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-    digest,
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-    gridExtra,
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-    methods,
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-    reshape2,
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-    MAST,
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-    S4Vectors,
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-    data.table,
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-    Rcpp,
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-    RcppArmadillo,
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-    RcppEigen,
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-    uwot,
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-    enrichR,
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-    stringi,
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-    SummarizedExperiment,
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-    MCMCprecision,
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-    ggrepel,
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-    Rtsne,
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-    withr,
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-    dendextend,
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-    ggdendro,
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-    pROC,
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-    scater (>= 1.14.4),
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-    scran,
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-    SingleCellExperiment,
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-    dbscan,
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-    DelayedArray,
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-    Seurat,
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-    stringr,
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-    Matrix
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-Suggests:
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-    testthat,
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-    knitr,
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-    roxygen2,
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-    rmarkdown,
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-    biomaRt,
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-    covr,
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-    BiocManager,
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-    BiocStyle,
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-    M3DExampleData,
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-    TENxPBMCData
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-LinkingTo: RcppArmadillo, Rcpp, RcppEigen
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+Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
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+        grDevices, graphics, matrixStats, doParallel, digest,
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+        gridExtra, methods, reshape2, MAST, S4Vectors, data.table,
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+        Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment,
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+        MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro,
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+        pROC, scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
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+        DelayedArray, Seurat, stringr, Matrix
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+Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
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+        BiocManager, BiocStyle, M3DExampleData, TENxPBMCData
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+LinkingTo: Rcpp, RcppEigen
68 24 
 License: MIT + file LICENSE
69 25 
 Encoding: UTF-8
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 LazyData: false
71 27 
 RoxygenNote: 7.1.0
72 28 
 BugReports: https://github.com/campbio/celda/issues
73 29 
 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian
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+NeedsCompilation: yes
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+Packaged: 2020-04-02 18:47:49 UTC; josh
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+Author: Joshua Campbell [aut, cre],
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+  Sean Corbett [aut],
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+  Yusuke Koga [aut],
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+  Shiyi Yang [aut],
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+  Eric Reed [aut],
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+  Zhe Wang [aut]
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+Maintainer: Joshua Campbell <camp@bu.edu>
Browse code

seqs -> seq

zhewa authored on 19/03/2020 09:32:17
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DESCRIPTION
History View file @ 658129a3
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.3.5
3 
+Version: 1.3.6
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

remove decontX vignette to fix timeout

zhewa authored on 17/03/2020 14:40:59
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DESCRIPTION
History View file @ 0d18701b
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@@ -1,6 +1,6 @@
1 1 
 Package: celda
2 2 
 Title: CEllular Latent Dirichlet Allocation
3 
-Version: 1.3.4
3 
+Version: 1.3.5
4 4 
 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
5 5 
     role = c("aut", "cre")),
6 6 
     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
Browse code

fix lints

zhewa authored on 17/03/2020 07:59:12
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DESCRIPTION
History View file @ e7fe6396
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@@ -68,6 +68,6 @@ LinkingTo: RcppArmadillo, Rcpp, RcppEigen
68 68 
 License: MIT + file LICENSE
69 69 
 Encoding: UTF-8
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 LazyData: false
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-RoxygenNote: 7.0.2
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+RoxygenNote: 7.1.0
72 72 
 BugReports: https://github.com/campbio/celda/issues
73 73 
 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian
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Merged findMarkersTree

Joshua D. Campbell authored on 13/03/2020 03:03:26
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merged vignette fixes

Joshua D. Campbell authored on 13/03/2020 00:44:31
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fix bug

zhewa authored on 05/03/2020 06:32:21
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DESCRIPTION
History View file @ bdb26ed8
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@@ -51,7 +51,8 @@ Imports:
51 51 
     scran,
52 52 
     SingleCellExperiment,
53 53 
     dbscan,
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-    DelayedArray
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+    DelayedArray,
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+    Ringo
55 56 
 Suggests:
56 57 
     testthat,
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     knitr,
Browse code

Updated docs. Fixed package referncing in celdaMarkerPlot. Updated DESCRIPTION.

Joshua D. Campbell authored on 02/03/2020 04:51:11
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DESCRIPTION
History View file @ 8374c3f6
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@@ -51,19 +51,19 @@ Imports:
51 51 
     scran,
52 52 
     SingleCellExperiment,
53 53 
     dbscan,
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-    DelayedArray
54 
+    DelayedArray,
55 
+    Matrix,
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+    M3DExampleData
55 57 
 Suggests:
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     testthat,
57 59 
     knitr,
58 60 
     roxygen2,
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     rmarkdown,
60 
-    Matrix,
61 62 
     biomaRt,
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     covr,
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-    M3DExampleData,
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     BiocManager,
65 65 
     BiocStyle
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-LinkingTo: Rcpp, RcppArmadillo, RcppEigen
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+LinkingTo: RcppArmadillo, Rcpp, RcppEigen
67