Merge pull request #3982 from satijalab/develop

Seurat v4.0.0

.Rbuildignore

@@ -8,3 +8,8 @@ azure-pipelines.yml
 cran-comments.md
 travis_setup.sh
 CODE_OF_CONDUCT.md
+^_pkgdown\.yaml$
+^docs$
+^pkgdown$
+^index\.md$
+^vignettes$

.github/workflows/R_CMD_check.yaml

@@ -17,9 +17,12 @@ jobs:
 
         steps:
             - uses: actions/checkout@v2
+            - name: Remove vignettes dir
+              run: rm -rf 'vignettes/'
+              shell: bash
 
             - name: Check
-              run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
+              run:  devtools::check(args = "--no-manual", error_on = "warning", check_dir = "check")
               shell: Rscript {0}
 
             - name: Upload check results

.gitignore

@@ -7,3 +7,4 @@ src/*.so
 src/*.dll
 .DS_Store
 *.pdf
+docs/

DESCRIPTION

@@ -1,25 +1,32 @@
 Package: Seurat
-Version: 3.2.3
-Date: 2020-12-14
+Version: 4.0.0
+Date: 2021-01-27
 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 Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.
+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>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> 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 = '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')),
-  person(given = 'Patrick', family = 'Roelli', email = 'proelli@nygenome.org', role = 'ctb'),
-  person(given = "Yuhan", family = "Hao", email = 'yhao@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0002-1810-0822'))
+  person(given = "Andrew", family = "Butler", email = "abutler@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-3608-0463")),
+  person(given = "Saket", family = "Choudhary", email = "schoudhary@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5202-7633")),
+  person(given = "Charlotte", family = "Darby", email = "cdarby@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-2195-5300")),
+  person(given = "Jeff", family = "Farrell", email = "jfarrell@g.harvard.edu", role = "ctb"),
+  person(given = "Christoph", family = "Hafemeister", email = "chafemeister@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-6365-8254")),
+  person(given = "Yuhan", family = "Hao", email = "yhao@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-1810-0822")),
+  person(given = "Paul", family = "Hoffman", email = "nygcSatijalab@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7693-8957")),
+  person(given = "Jaison", family = "Jain", email = "jjain@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")),
+  person(given = "Efthymia", family = "Papalexi", email = "epapalexi@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5898-694X")),
+  person(given = "Patrick", family = "Roelli", email = "proelli@nygenome.org", role = "ctb"),
+  person(given = "Rahul", family = "Satija", email = "rsatija@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-9448-8833")),
+  person(given = "Karthik", family = "Shekhar", email = "kshekhar@berkeley.edu", role = "ctb"),
+  person(given = "Avi", family = "Srivastava", email = "asrivastava@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-9798-2079")),
+  person(given = "Tim", family = "Stuart", email = "tstuart@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-3044-0897")),
+  person(given = "Kristof", family = "Torkenczy", email = "", role = "ctb", comment = c(ORCID = "0000-0002-4869-7957")),
+  person(given = "Shiwei", family = "Zheng", email = "szheng@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-6682-6743")),
+  person("Satija Lab and Collaborators", role = "fnd")
   )
 URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat
 BugReports: https://github.com/satijalab/seurat/issues
-Additional_repositories: https://mojaveazure.github.io/loomR
 Depends:
-    R (>= 3.6.0),
-    methods,
+    R (>= 4.0.0),
+    methods
 Imports:
     cluster,
     cowplot,
@@ -51,15 +58,15 @@ Imports:
     RANN,
     RColorBrewer,
     Rcpp,
-    RcppAnnoy,
+    RcppAnnoy (>= 0.0.18),
     reticulate,
     rlang,
     ROCR,
-    rsvd,
     Rtsne,
     scales,
     scattermore (>= 0.7),
-    sctransform (>= 0.3.1),
+    sctransform (>= 0.3.2),
+    SeuratObject,
     shiny,
     spatstat,
     stats,
@@ -72,6 +79,7 @@ License: GPL-3 | file LICENSE
 LazyData: true
 Collate:
     'RcppExports.R'
+    'reexports.R'
     'generics.R'
     'clustering.R'
     'visualization.R'
@@ -80,6 +88,7 @@ Collate:
     'differential_expression.R'
     'dimensional_reduction.R'
     'integration.R'
+    'mixscape.R'
     'objects.R'
     'preprocessing.R'
     'tree.R'
@@ -88,8 +97,8 @@ Collate:
 RoxygenNote: 7.1.1
 Encoding: UTF-8
 Suggests:
-    loomR,
     ape,
+    rsvd,
     testthat,
     hdf5r,
     S4Vectors,
@@ -107,4 +116,6 @@ Suggests:
     Biobase,
     VGAM,
     limma,
-    metap
+    metap,
+    enrichR,
+    mixtools