Merge pull request #1375 from satijalab/release/3.0

Seurat v3

.Rbuildignore

@@ -1,5 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^.*\.old$
 .git
 .travis.yml
 appveyor.yml

.travis.yml

@@ -30,14 +30,17 @@ addons:
       - build-essential
       - libtool
       - libmagick++-dev
-
-bioc_packages:
-  - GenomeInfoDbData
-  - DESeq2
-  - MAST
-  - S4Vectors
-  - SummarizedExperiment
-  - SingleCellExperiment
+  homebrew:
+    packages:
+      - libgit2
+
+#bioc_packages:
+#  - GenomeInfoDbData
+#  - DESeq2
+#  - MAST
+#  - S4Vectors
+#  - SummarizedExperiment
+#  - SingleCellExperiment
 
 r_github_packages:
   - mojaveazure/loomR

DESCRIPTION

@@ -1,12 +1,13 @@
 Package: Seurat
-Version: 2.3.3
-Date: 2018-07-02
+Version: 3.0.0
+Date: 2019-04-16
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Andrew', family = 'Butler', email = 'abutler@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),
-  person(given = 'Paul', family = 'Hoffman', email = 'seuratpackage@gmail.com', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-7693-8957')),
+  person(given = 'Paul', family = 'Hoffman', email = 'nygcSatijalab@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-7693-8957')),
+  person(given = 'Tim', family = 'Stuart', email = 'tstuart@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0002-3044-0897')),
   person(given = 'Jeff', family = 'Farrell', email = 'jfarrell@g.harvard.edu', role = 'ctb'),
   person(given = 'Shiwei', family = 'Zheng', email = 'szheng@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-6682-6743')),
   person(given = 'Christoph', family = 'Hafemeister', email = 'chafemeister@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-6365-8254')),
@@ -17,95 +18,75 @@ BugReports: https://github.com/satijalab/seurat/issues
 Additional_repositories: https://mojaveazure.github.io/loomR
 Depends:
     R (>= 3.4.0),
-    ggplot2,
-    cowplot,
-    Matrix (>= 1.2.14),
-SystemRequirements: Java (>= 6)
-Imports:
     methods,
-    ROCR,
-    mixtools,
-    lars,
-    ica,
-    tsne,
-    Rtsne,
-    fpc,
+Imports:
     ape,
-    pbapply,
+    cluster,
+    cowplot,
+    fitdistrplus,
+    future,
+    future.apply,
+    ggplot2 (>= 3.0.0),
+    ggrepel,
+    ggridges,
+    graphics,
+    grDevices,
+    grid,
+    ica,
     igraph,
-    RANN,
-    dplyr,
-    RColorBrewer,
-    MASS,
     irlba,
-    reshape2,
-    gplots,
-    Rcpp (>= 0.11.0),
-    dtw,
-    SDMTools,
-    plotly,
-    diffusionMap,
-    Hmisc,
-    tidyr,
-    ggridges,
-    metap,
+    KernSmooth,
     lmtest,
-    cluster,
-    fitdistrplus,
+    MASS,
+    Matrix (>= 1.2.14),
+    metap,
+    pbapply,
+    plotly,
     png,
-    doSNOW,
+    RANN,
+    RColorBrewer,
+    Rcpp,
     reticulate,
-    foreach,
-    hdf5r
+    rlang,
+    ROCR,
+    rsvd,
+    Rtsne,
+    scales,
+    sctransform (>= 0.2.0),
+    SDMTools,
+    stats,
+    tools,
+    tsne,
+    utils
 LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress
 License: GPL-3 | file LICENSE
 LazyData: true
 Collate:
     'RcppExports.R'
-    'alignment.R'
-    'seurat.R'
-    'conversion.R'
-    'as.R'
-    'cluster_determination.R'
-    'cluster_determination_internal.R'
-    'cluster_validation.R'
+    'generics.R'
+    'clustering.R'
+    'visualization.R'
+    'convenience.R'
     'data.R'
-    'deprecated_functions.R'
     'differential_expression.R'
-    'differential_expression_internal.R'
     'dimensional_reduction.R'
-    'dimensional_reduction_internal.R'
-    'dimensional_reduction_utilities.R'
-    'interaction.R'
-    'jackstraw.R'
-    'jackstraw_internal.R'
-    'multi_modal.R'
-    'plotting.R'
-    'plotting_internal.R'
-    'plotting_utilities.R'
+    'integration.R'
+    'objects.R'
     'preprocessing.R'
-    'preprocessing_internal.R'
-    'printing_utilities.R'
-    'scoring.R'
-    'snn.R'
-    'spatial.R'
-    'spatial_internal.R'
-    'tSNE_project.R'
+    'tree.R'
     'utilities.R'
-    'utilities_internal.R'
-    'zfRenderSeurat.R'
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1
+Encoding: UTF-8
 Suggests:
-    gdata,
-    VGAM,
-    tclust,
-    testthat,
-    caret,
-    ranger,
     loomR,
-    phateR,
+    testthat,
+    hdf5r,
     S4Vectors,
     SummarizedExperiment,
     SingleCellExperiment,
     MAST,
-    DESeq2
+    DESeq2,
+    GenomicRanges,
+    GenomeInfoDb,
+    IRanges,
+    rtracklayer