1. CellaRepertorium
  2. DESCRIPTION
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bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:23:20
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DESCRIPTION
History View file @ de926ef
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
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     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.8.0
5 
+Version: 1.9.0
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
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 15:23:20
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DESCRIPTION
History View file @ 5346a3b
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
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     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.7.1
5 
+Version: 1.8.0
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

Bump, I guess?

Andrew McDavid authored on 20/04/2022 16:34:43
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DESCRIPTION
History View file @ c9401d2
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.7.0
5 
+Version: 1.7.1
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

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

Nitesh Turaga authored on 26/04/2022 16:10:29 • Andrew McDavid committed on 10/05/2022 15:28:10
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DESCRIPTION
History View file @ cfa9d7d
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.6.0
5 
+Version: 1.7.0
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
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 16:10:29 • Andrew McDavid committed on 10/05/2022 15:28:08
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DESCRIPTION
History View file @ c44ca63
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.5.1
5 
+Version: 1.6.0
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

Handle missing contrast names

Andrew McDavid authored on 10/05/2022 14:32:14
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DESCRIPTION
History View file @ 133e12c
... ... 
@@ -49,7 +49,8 @@ Imports:
49 49 
     progress,
50 50 
     stats,
51 51 
     utils,
52 
-    generics
52 
+    generics,
53 
+    glue
53 54 
 Suggests:
54 55 
     testthat,
55 56 
     readr,
Browse code

Bump, I guess?

Andrew McDavid authored on 20/04/2022 16:34:43
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DESCRIPTION
History View file @ d17a5e7
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.5.0
5 
+Version: 1.5.1
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

Tried a bunch of stuff to try to get the tidy method found. Finally gave up and exported tidy.* Pretty sure there's a bug in R I'm hitting here...

Andrew McDavid authored on 20/04/2022 16:29:41
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DESCRIPTION
History View file @ 1a7ddf0
... ... 
@@ -79,3 +79,22 @@ BugReports: https://github.com/amcdavid/CellaRepertorium/issues
79 79 
 Roxygen: list(markdown = TRUE)
80 80 
 biocViews: RNASeq, Transcriptomics, SingleCell, TargetedResequencing,
81 81 
     Technology, ImmunoOncology, Clustering
82 
+Collate:
83 
+    'AllClasses.R'
84 
+    'ContigCellDB-methods.R'
85 
+    'RcppExports.R'
86 
+    'auxiliary.R'
87 
+    'ccdb_join.R'
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+    'cdhit-methods.R'
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+    'cluster-testing.R'
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+    'clustering-methods.R'
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+    'data.R'
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+    'ggplot2-utils.R'
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+    'pairing-methods.R'
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+    'reexports.R'
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+    'permutation-testing.R'
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+    'plot_clustering.R'
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+    'plotting.R'
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+    'pseudo-bulk.R'
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+    'utilty.R'
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+    'vdjcellranger-methods.R'
Browse code

Support for vector-valued permutation statistics + contrasts therein

Andrew McDavid authored on 15/04/2022 02:04:02
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DESCRIPTION
History View file @ c4d88a3
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@@ -48,7 +48,8 @@ Imports:
48 48 
     forcats,
49 49 
     progress,
50 50 
     stats,
51 
-    utils
51 
+    utils,
52 
+    generics
52 53 
 Suggests:
53 54 
     testthat,
54 55 
     readr,
Browse code

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

Nitesh Turaga authored on 26/10/2021 17:04:40
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DESCRIPTION
History View file @ 2f16fab
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.4.0
5 
+Version: 1.5.0
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
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 17:04:40
Showing 1 changed files
DESCRIPTION
History View file @ ee7f173
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.3.1
5 
+Version: 1.4.0
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

potential speed up in cland

Andrew McDavid authored on 28/09/2021 20:36:56
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DESCRIPTION
History View file @ dfaded1
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.3.0
5 
+Version: 1.3.1
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
... ... 
@@ -72,7 +72,7 @@ VignetteBuilder:
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     knitr
73 73 
 Encoding: UTF-8
74 74 
 NeedsCompilation: yes
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-RoxygenNote: 7.1.1
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+RoxygenNote: 7.1.2
76 76 
 URL: https://github.com/amcdavid/CellaRepertorium
77 77 
 BugReports: https://github.com/amcdavid/CellaRepertorium/issues
78 78 
 Roxygen: list(markdown = TRUE)
Browse code

Bump version

Merge branch 'master' of git.bioconductor.org:packages/CellaRepertorium into master

# Conflicts:
# DESCRIPTION

Andrew McDavid authored on 29/07/2021 15:17:15
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Browse code

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

Nitesh Turaga authored on 19/05/2021 16:57:31
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DESCRIPTION
History View file @ 730c662
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
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     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.2.0
5 
+Version: 1.3.0
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
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 16:57:31
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DESCRIPTION
History View file @ 86b7f10
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.1.2
5 
+Version: 1.2.0
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 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
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check for fine_clustering and emit warning

Andrew McDavid authored on 07/04/2021 14:19:40
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DESCRIPTION
History View file @ 328e977
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@@ -16,6 +16,9 @@ Authors@R:
16 16 
       family = 'VonKaenel',
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       role = 'aut'
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       ),
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+      person(given = 'Aaron',
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+      family = 'Wagner',
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+      role = 'aut'),
19 22 
       person(given = 'Thomas Lin',
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              family = 'Pedersen',
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              role = 'ctb'))
Browse code

Cleanup plot_clustering. More sanity checks, add packages to Suggests

Andrew McDavid authored on 07/04/2021 05:12:34
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DESCRIPTION
History View file @ befdd6f
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.1.2
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+Version: 1.1.3
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 Authors@R:
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     c(person(given = "Andrew",
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              family = "McDavid",
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@@ -60,7 +60,9 @@ Suggests:
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     SingleCellExperiment,
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     scater,
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     broom.mixed,
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-    cowplot
63 
+    cowplot,
64 
+    igraph,
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+    ggraph
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 LinkingTo:
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     Rcpp
66 68 
 VignetteBuilder:
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bump

Andrew McDavid authored on 22/11/2020 21:24:05
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DESCRIPTION
History View file @ ddcab24
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.1.1
5 
+Version: 1.1.2
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

Fixes #6

Andrew McDavid authored on 05/11/2020 22:32:06
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DESCRIPTION
History View file @ dd80804
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.1.0
5 
+Version: 1.1.1
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

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

Nitesh Turaga authored on 27/10/2020 16:03:47
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DESCRIPTION
History View file @ 7781b69
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 1.0.0
5 
+Version: 1.1.0
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
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 16:03:47
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DESCRIPTION
History View file @ 4e5b113
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 0.99.6
5 
+Version: 1.0.0
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
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alpha not available on the graphics device of the Bioc builder

Andrew McDavid authored on 20/10/2020 18:19:16
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DESCRIPTION
History View file @ 7614de8
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 0.99.5
5 
+Version: 0.99.6
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 Authors@R:
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     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

Expand/cleanup cdr3 clustering vignette Add cluster_plot function Add a (somewhat fragile) function to test if fine_clustering has been run.

Andrew McDavid authored on 19/10/2020 20:32:40
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DESCRIPTION
History View file @ 6432de0
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 0.99.4
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+Version: 0.99.5
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 Authors@R:
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     c(person(given = "Andrew",
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              family = "McDavid",
... ... 
@@ -59,7 +59,8 @@ Suggests:
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     RColorBrewer,
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     SingleCellExperiment,
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     scater,
62 
-    broom.mixed
62 
+    broom.mixed,
63 
+    cowplot
63 64 
 LinkingTo:
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     Rcpp
65 66 
 VignetteBuilder:
Browse code

Import from BiocGenerics so that S4Vectors makes its nrow/ncol methods properly.

Confused why this is necessary, but fixes an infinite loop in S4Vectors methods dispatch in the unit tests.

Andrew McDavid authored on 15/10/2020 14:26:35
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DESCRIPTION
History View file @ 6c82e73
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@@ -40,6 +40,7 @@ Imports:
40 40 
     purrr,
41 41 
     Matrix,
42 42 
     S4Vectors,
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+    BiocGenerics,
43 44 
     tidyr,
44 45 
     forcats,
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     progress,
Browse code

cast template to data.frame

Andrew McDavid authored on 08/10/2020 18:13:00
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DESCRIPTION
History View file @ 68099a7
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 0.99.3
5 
+Version: 0.99.4
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 Authors@R:
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     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

add example to generate_pseudobulk

Andrew McDavid authored on 06/10/2020 04:42:41
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DESCRIPTION
History View file @ 698d1fb
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
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     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 0.99.2
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+Version: 0.99.3
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 Authors@R:
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     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

Bumpity bumpity, hold on tight.

Andrew McDavid authored on 01/10/2020 21:32:32
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DESCRIPTION
History View file @ 33a826f
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 0.99.1
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+Version: 0.99.2
6 6 
 Authors@R:
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     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

Rbuildignore WORDLIST Lazydata: FALSE Fix a few spelling errors

Andrew McDavid authored on 30/09/2020 18:11:48
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DESCRIPTION
History View file @ 7840144
... ... 
@@ -64,7 +64,6 @@ LinkingTo:
64 64 
 VignetteBuilder:
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     knitr
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 Encoding: UTF-8
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-LazyData: true
68 67 
 NeedsCompilation: yes
69 68 
 RoxygenNote: 7.1.1
70 69 
 URL: https://github.com/amcdavid/CellaRepertorium
Browse code

Hopefully quell errors about access to functions w/o IMPORTing in BiocCheck

Start to use .data pronoun to avoid NOTES about dplyr syntax. This likely ends use of this package for R <= 3.5.

Andrew McDavid authored on 08/09/2020 20:57:55
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DESCRIPTION
History View file @ 608f89f
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 0.99.0
5 
+Version: 0.99.1
6 6 
 Authors@R:
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     c(person(given = "Andrew",
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              family = "McDavid",
... ... 
@@ -27,7 +27,7 @@ Description: Methods to cluster and analyze high-throughput
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     hypergeometric models.
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 License: GPL-3
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 Depends:
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-    R (>= 3.5.0)
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+    R (>= 4.0)
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 Imports:
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     dplyr,
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     tibble,
... ... 
@@ -36,7 +36,7 @@ Imports:
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     Rcpp,
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     reshape2,
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     methods,
39 
-    rlang,
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+    rlang (>= 0.3),
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     purrr,
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     Matrix,
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     S4Vectors,
Browse code

Bump version Chant a propalytic Rcpp spell (probably relating to ABI mismatches somewhere on my machine?) Check for broom.mixed (should be deprecated eventually)

Andrew McDavid authored on 03/09/2020 21:17:25
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DESCRIPTION
History View file @ a32b7c8
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
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     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 0.98.3
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+Version: 0.99.0
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
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              family = "McDavid",
... ... 
@@ -12,6 +12,10 @@ Authors@R:
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              family = "Gu",
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              role = "aut",
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              email = "Yu_Gu@urmc.rochester.edu"),
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+      person(given = 'Erik',
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+      family = 'VonKaenel',
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+      role = 'aut'
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+      ),
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       person(given = 'Thomas Lin',
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              family = 'Pedersen',
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              role = 'ctb'))
... ... 
@@ -53,7 +57,8 @@ Suggests:
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     lme4,
54 58 
     RColorBrewer,
55 59 
     SingleCellExperiment,
56 
-    scater
60 
+    scater,
61 
+    broom.mixed
57 62 
 LinkingTo:
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     Rcpp
59 64 
 VignetteBuilder:
... ... 
@@ -61,7 +66,7 @@ VignetteBuilder:
61 66 
 Encoding: UTF-8
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 LazyData: true
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 NeedsCompilation: yes
64 
-RoxygenNote: 7.1.0
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+RoxygenNote: 7.1.1
65 70 
 URL: https://github.com/amcdavid/CellaRepertorium
66 71 
 BugReports: https://github.com/amcdavid/CellaRepertorium/issues
67 72 
 Roxygen: list(markdown = TRUE)
Browse code

Fixes to handle changes in dplyr 1.0

Andrew McDavid authored on 10/06/2020 20:07:33
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DESCRIPTION
History View file @ 31f54ba
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
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     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
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-Version: 0.98.2
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+Version: 0.98.3
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 Authors@R:
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     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

add function to get and color ggplot2 axes labels

Andrew McDavid authored on 18/05/2020 18:23:43
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DESCRIPTION
History View file @ fbb51dc
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 0.98.1
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+Version: 0.98.2
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 Authors@R:
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     c(person(given = "Andrew",
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              family = "McDavid",
... ... 
@@ -61,7 +61,7 @@ VignetteBuilder:
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 Encoding: UTF-8
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 LazyData: true
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 NeedsCompilation: yes
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-RoxygenNote: 7.0.2
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+RoxygenNote: 7.1.0
65 65 
 URL: https://github.com/amcdavid/CellaRepertorium
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 BugReports: https://github.com/amcdavid/CellaRepertorium/issues
67 67 
 Roxygen: list(markdown = TRUE)
Browse code

bump version

Andrew McDavid authored on 08/01/2020 07:08:59
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DESCRIPTION
History View file @ 99d0439
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
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     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
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-Version: 0.98.0
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+Version: 0.98.1
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 Authors@R:
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     c(person(given = "Andrew",
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              family = "McDavid",
Browse code

Update calls to scater for bioc devel

Andrew McDavid authored on 08/01/2020 05:54:48
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DESCRIPTION
History View file @ 1d39cfa
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@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
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 Title: Data structures, clustering and testing for single
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     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
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-Version: 0.8.1
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+Version: 0.98.0
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 Authors@R:
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     c(person(given = "Andrew",
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              family = "McDavid",
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@@ -61,7 +61,7 @@ VignetteBuilder:
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 Encoding: UTF-8
62 62 
 LazyData: true
63 63 
 NeedsCompilation: yes
64 
-RoxygenNote: 6.1.1
64 
+RoxygenNote: 7.0.2
65 65 
 URL: https://github.com/amcdavid/CellaRepertorium
66 66 
 BugReports: https://github.com/amcdavid/CellaRepertorium/issues
67 67 
 Roxygen: list(markdown = TRUE)
Browse code

LazyData: true needed for data to be automatically in package NAMESPACE, I guess?

Andrew McDavid authored on 05/09/2019 18:57:50
Showing 1 changed files
DESCRIPTION
History View file @ 3257fe9
... ... 
@@ -59,6 +59,7 @@ LinkingTo:
59 59 
 VignetteBuilder:
60 60 
     knitr
61 61 
 Encoding: UTF-8
62 
+LazyData: true
62 63 
 NeedsCompilation: yes
63 64 
 RoxygenNote: 6.1.1
64 65 
 URL: https://github.com/amcdavid/CellaRepertorium
Browse code

bump version

Andrew McDavid authored on 05/09/2019 18:07:19
Showing 1 changed files
DESCRIPTION
History View file @ e3b1981
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 0.8.0
5 
+Version: 0.8.1
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

Move data/manuscript prep to CellaRepertoriumData

Andrew McDavid authored on 05/09/2019 17:53:25
Showing 1 changed files
DESCRIPTION
History View file @ 03b3287
... ... 
@@ -59,7 +59,6 @@ LinkingTo:
59 59 
 VignetteBuilder:
60 60 
     knitr
61 61 
 Encoding: UTF-8
62 
-LazyData: true
63 62 
 NeedsCompilation: yes
64 63 
 RoxygenNote: 6.1.1
65 64 
 URL: https://github.com/amcdavid/CellaRepertorium
Browse code

Hopefully much faster canonicalization And more BiocCheck attempts

Andrew McDavid authored on 02/09/2019 05:02:39
Showing 1 changed files
DESCRIPTION
History View file @ 49b2df2
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Data structures, clustering and testing for single
4 4 
     cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
-Version: 0.4.0
5 
+Version: 0.8.0
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

Start to address BiocCheck

Andrew McDavid authored on 02/09/2019 04:34:06
Showing 1 changed files
DESCRIPTION
History View file @ d507c94
... ... 
@@ -11,8 +11,10 @@ Authors@R:
11 11 
       person(given = "Yu",
12 12 
              family = "Gu",
13 13 
              role = "aut",
14 
-             email = "Yu_Gu@urmc.rochester.edu"))
15 
-Maintainer: Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
14 
+             email = "Yu_Gu@urmc.rochester.edu"),
15 
+      person(given = 'Thomas Lin',
16 
+             family = 'Pedersen',
17 
+             role = 'ctb'))
16 18 
 Description: Methods to cluster and analyze high-throughput
17 19 
     single cell immune cell repertoires, especially from the 10X Genomics
18 20 
     VDJ solution. Contains an R interface to CD-HIT (Li and Godzik 2006).
... ... 
@@ -36,7 +38,9 @@ Imports:
36 38 
     S4Vectors,
37 39 
     tidyr,
38 40 
     forcats,
39 
-    progress
41 
+    progress,
42 
+    stats,
43 
+    utils
40 44 
 Suggests:
41 45 
     testthat,
42 46 
     readr,
... ... 
@@ -61,3 +65,5 @@ RoxygenNote: 6.1.1
61 65 
 URL: https://github.com/amcdavid/CellaRepertorium
62 66 
 BugReports: https://github.com/amcdavid/CellaRepertorium/issues
63 67 
 Roxygen: list(markdown = TRUE)
68 
+biocViews: RNASeq, Transcriptomics, SingleCell, TargetedResequencing,
69 
+    Technology, ImmunoOncology, Clustering
Browse code

Many changes about equalization to try to preserve length of cell_tbl 1. Add equalize argument to constructor 2. Don't equalize cells if contigs replaced 3. Don't equalize if cluster table is replaced 4. split_cdb gains an equalization argument

Andrew McDavid authored on 28/08/2019 03:25:45
Showing 1 changed files
DESCRIPTION
History View file @ 5a52904
... ... 
@@ -47,7 +47,9 @@ Suggests:
47 47 
     ggdendro,
48 48 
     broom,
49 49 
     lme4,
50 
-    RColorBrewer
50 
+    RColorBrewer,
51 
+    SingleCellExperiment,
52 
+    scater
51 53 
 LinkingTo:
52 54 
     Rcpp
53 55 
 VignetteBuilder:
Browse code

doc updates

Andrew McDavid authored on 22/08/2019 17:54:00
Showing 1 changed files
DESCRIPTION
History View file @ 4688031
... ... 
@@ -1,8 +1,8 @@
1 1 
 Type: Package
2 2 
 Package: CellaRepertorium
3 
-Title: Methods for clustering and analyzing high-throughput
4 
-    single cell immune cell repertoires (RepSeq)
5 
-Version: 0.3.4
3 
+Title: Data structures, clustering and testing for single
4 
+    cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
5 
+Version: 0.4.0
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
... ... 
@@ -35,7 +35,8 @@ Imports:
35 35 
     Matrix,
36 36 
     S4Vectors,
37 37 
     tidyr,
38 
-    forcats
38 
+    forcats,
39 
+    progress
39 40 
 Suggests:
40 41 
     testthat,
41 42 
     readr,
Browse code

Logistic/glmer tests of clusters

Andrew McDavid authored on 05/08/2019 14:16:01
Showing 1 changed files
DESCRIPTION
History View file @ d5334e6
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Methods for clustering and analyzing high-throughput
4 4 
     single cell immune cell repertoires (RepSeq)
5 
-Version: 0.3.3
5 
+Version: 0.3.4
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

Doc updates

Andrew McDavid authored on 25/06/2019 03:31:34
Showing 1 changed files
DESCRIPTION
History View file @ d05fd6e
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Methods for clustering and analyzing high-throughput
4 4 
     single cell immune cell repertoires (RepSeq)
5 
-Version: 0.3.2
5 
+Version: 0.3.3
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

Doc polishing

Andrew McDavid authored on 21/06/2019 15:24:37
Showing 1 changed files
DESCRIPTION
History View file @ be99b48
... ... 
@@ -57,3 +57,4 @@ NeedsCompilation: yes
57 57 
 RoxygenNote: 6.1.1
58 58 
 URL: https://github.com/amcdavid/CellaRepertorium
59 59 
 BugReports: https://github.com/amcdavid/CellaRepertorium/issues
60 
+Roxygen: list(markdown = TRUE)
Browse code

doc updates (II)

Andrew McDavid authored on 21/06/2019 04:18:56
Showing 1 changed files
DESCRIPTION
History View file @ 07cf25d
... ... 
@@ -2,7 +2,7 @@ Type: Package
2 2 
 Package: CellaRepertorium
3 3 
 Title: Methods for clustering and analyzing high-throughput
4 4 
     single cell immune cell repertoires (RepSeq)
5 
-Version: 0.3.1
5 
+Version: 0.3.2
6 6 
 Authors@R:
7 7 
     c(person(given = "Andrew",
8 8 
              family = "McDavid",
Browse code

Use pkgdown to make website

Andrew McDavid authored on 19/06/2019 14:15:03
Showing 1 changed files
DESCRIPTION
History View file @ 31cd01a
... ... 
@@ -55,3 +55,5 @@ Encoding: UTF-8
55 55 
 LazyData: true
56 56 
 NeedsCompilation: yes
57 57 
 RoxygenNote: 6.1.1
58 
+URL: https://github.com/amcdavid/CellaRepertorium
59 
+BugReports: https://github.com/amcdavid/CellaRepertorium/issues
Browse code

Doc/example updates

Andrew McDavid authored on 19/06/2019 06:04:46
Showing 1 changed files
DESCRIPTION
History View file @ d31ff2a
... ... 
@@ -1,31 +1,41 @@
1 
-Package: CellaRepertorium
2 1 
 Type: Package
3 
-Title: Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)
4 
-Version: 0.3.0
5 
-Author: Andrew McDavid
2 
+Package: CellaRepertorium
3 
+Title: Methods for clustering and analyzing high-throughput
4 
+    single cell immune cell repertoires (RepSeq)
5 
+Version: 0.3.1
6 
+Authors@R:
7 
+    c(person(given = "Andrew",
8 
+             family = "McDavid",
9 
+             role = c('aut', 'cre'),
10 
+             email = "Andrew_McDavid@urmc.rochester.edu"),
11 
+      person(given = "Yu",
12 
+             family = "Gu",
13 
+             role = "aut",
14 
+             email = "Yu_Gu@urmc.rochester.edu"))
6 15 
 Maintainer: Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
7 
-Description: Methods to cluster and analyze high-throughput single cell immune cell repertoires,
8 
-    especially from the 10X Genomics VDJ solution.
9 
-    Contains an R interface to CD-HIT (Li and Godzik 2006).
10 
-    Tests for specific expansion, as well as omnibus oligoclonality under hypergeometric models.
16 
+Description: Methods to cluster and analyze high-throughput
17 
+    single cell immune cell repertoires, especially from the 10X Genomics
18 
+    VDJ solution. Contains an R interface to CD-HIT (Li and Godzik 2006).
19 
+    Methods to visualize and analyze paired heavy-light chain data.
20 
+    Tests for specific expansion, as well as omnibus oligoclonality under
21 
+    hypergeometric models.
11 22 
 License: GPL-3
12 
-Encoding: UTF-8
13 
-LazyData: true
14 
-Depends: R (>= 3.5.0)
23 
+Depends:
24 
+    R (>= 3.5.0)
15 25 
 Imports:
16 
-   dplyr,
17 
-   tibble,
18 
-   stringr,
19 
-   Biostrings,
20 
-   Rcpp,
21 
-   reshape2,
22 
-   methods,
23 
-   rlang,
24 
-   purrr,
25 
-   Matrix,
26 
-   S4Vectors,
27 
-   tidyr,
28 
-   forcats
26 
+    dplyr,
27 
+    tibble,
28 
+    stringr,
29 
+    Biostrings,
30 
+    Rcpp,
31 
+    reshape2,
32 
+    methods,
33 
+    rlang,
34 
+    purrr,
35 
+    Matrix,
36 
+    S4Vectors,
37 
+    tidyr,
38 
+    forcats
29 39 
 Suggests:
30 40 
     testthat,
31 41 
     readr,
... ... 
@@ -33,8 +43,15 @@ Suggests:
33 43 
     rmarkdown,
34 44 
     ggplot2,
35 45 
     BiocStyle,
36 
-    ggdendro
37 
-RoxygenNote: 6.1.1
38 
-LinkingTo: Rcpp
46 
+    ggdendro,
47 
+    broom,
48 
+    lme4,
49 
+    RColorBrewer
50 
+LinkingTo:
51 
+    Rcpp
52 
+VignetteBuilder:
53 
+    knitr
54 
+Encoding: UTF-8
55 
+LazyData: true
39 56 
 NeedsCompilation: yes
40 
-VignetteBuilder: knitr
57 
+RoxygenNote: 6.1.1
Browse code

Removing cluster_tbls slot and Clustering class. Now each ccdb can have at most one clustering.

Andrew McDavid authored on 17/06/2019 15:26:43
Showing 1 changed files
DESCRIPTION
History View file @ 1f5cfb6
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: CellaRepertorium
2 2 
 Type: Package
3 3 
 Title: Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)
4 
-Version: 0.2.4
4 
+Version: 0.3.0
5 5 
 Author: Andrew McDavid
6 6 
 Maintainer: Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
7 7 
 Description: Methods to cluster and analyze high-throughput single cell immune cell repertoires,
... ... 
@@ -24,7 +24,8 @@ Imports:
24 24 
    purrr,
25 25 
    Matrix,
26 26 
    S4Vectors,
27 
-   tidyr
27 
+   tidyr,
28 
+   forcats
28 29 
 Suggests:
29 30 
     testthat,
30 31 
     readr,
Browse code

Doc/data/NAMESPACE updates

Andrew McDavid authored on 11/06/2019 18:49:27
Showing 1 changed files
DESCRIPTION
History View file @ 02a4bac
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: CellaRepertorium
2 2 
 Type: Package
3 3 
 Title: Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)
4 
-Version: 0.2.3
4 
+Version: 0.2.4
5 5 
 Author: Andrew McDavid
6 6 
 Maintainer: Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
7 7 
 Description: Methods to cluster and analyze high-throughput single cell immune cell repertoires,
... ... 
@@ -23,7 +23,8 @@ Imports:
23 23 
    rlang,
24 24 
    purrr,
25 25 
    Matrix,
26 
-   S4Vectors
26 
+   S4Vectors,
27 
+   tidyr
27 28 
 Suggests:
28 29 
     testthat,
29 30 
     readr,
... ... 
@@ -31,7 +32,7 @@ Suggests:
31 32 
     rmarkdown,
32 33 
     ggplot2,
33 34 
     BiocStyle,
34 
-    tidyr
35 
+    ggdendro
35 36 
 RoxygenNote: 6.1.1
36 37 
 LinkingTo: Rcpp
37 38 
 NeedsCompilation: yes
Browse code

Organize ContigCellDB methods vs class

Andrew McDavid authored on 07/06/2019 21:59:58
Showing 1 changed files
DESCRIPTION
History View file @ 6f29fef
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: CellaRepertorium
2 2 
 Type: Package
3 3 
 Title: Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)
4 
-Version: 0.2.2
4 
+Version: 0.2.3
5 5 
 Author: Andrew McDavid
6 6 
 Maintainer: Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
7 7 
 Description: Methods to cluster and analyze high-throughput single cell immune cell repertoires,
Browse code

Update docs Bump version Require 3.5 (as data was serialized in v3)

Andrew McDavid authored on 02/06/2019 04:33:47
Showing 1 changed files
DESCRIPTION
History View file @ efd7d3a
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: CellaRepertorium
2 2 
 Type: Package
3 3 
 Title: Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)
4 
-Version: 0.2.1
4 
+Version: 0.2.2
5 5 
 Author: Andrew McDavid
6 6 
 Maintainer: Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
7 7 
 Description: Methods to cluster and analyze high-throughput single cell immune cell repertoires,
... ... 
@@ -11,6 +11,7 @@ Description: Methods to cluster and analyze high-throughput single cell immune c
11 11 
 License: GPL-3
12 12 
 Encoding: UTF-8
13 13 
 LazyData: true
14 
+Depends: R (>= 3.5.0)
14 15 
 Imports:
15 16 
    dplyr,
16 17 
    tibble,
... ... 
@@ -21,10 +22,17 @@ Imports:
21 22 
    methods,
22 23 
    rlang,
23 24 
    purrr,
24 
-   Matrix
25 
+   Matrix,
26 
+   S4Vectors
25 27 
 Suggests:
26 
-   testthat,
27 
-   readr
28 
-RoxygenNote: 6.1.0
28 
+    testthat,
29 
+    readr,
30 
+    knitr,
31 
+    rmarkdown,
32 
+    ggplot2,
33 
+    BiocStyle,
34 
+    tidyr
35 
+RoxygenNote: 6.1.1
29 36 
 LinkingTo: Rcpp
30 37 
 NeedsCompilation: yes
38 
+VignetteBuilder: knitr
Browse code

cdhit prefers user-provided options if given but tries to set reasonable defaults for some that had weird choices made by cdhit by default

Andrew McDavid authored on 02/04/2019 16:06:03
Showing 1 changed files
DESCRIPTION
History View file @ ffedfde
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: CellaRepertorium
2 2 
 Type: Package
3 3 
 Title: Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)
4 
-Version: 0.2.0
4 
+Version: 0.2.1
5 5 
 Author: Andrew McDavid
6 6 
 Maintainer: Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
7 7 
 Description: Methods to cluster and analyze high-throughput single cell immune cell repertoires,
Browse code

Update docs

Andrew McDavid authored on 14/03/2019 22:53:22
Showing 1 changed files
DESCRIPTION
History View file @ 66eb479
... ... 
@@ -1,25 +1,30 @@
1 1 
 Package: CellaRepertorium
2 2 
 Type: Package
3 3 
 Title: Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)
4 
-Version: 0.1.0
4 
+Version: 0.2.0
5 5 
 Author: Andrew McDavid
6 6 
 Maintainer: Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
7 7 
 Description: Methods to cluster and analyze high-throughput single cell immune cell repertoires,
8 8 
     especially from the 10X Genomics VDJ solution.
9 
+    Contains an R interface to CD-HIT (Li and Godzik 2006).
9 10 
     Tests for specific expansion, as well as omnibus oligoclonality under hypergeometric models.
10 11 
 License: GPL-3
11 12 
 Encoding: UTF-8
12 13 
 LazyData: true
13 14 
 Imports:
14 
-   httr,
15 
-   readr,
16 15 
    dplyr,
17 16 
    tibble,
18 17 
    stringr,
19 18 
    Biostrings,
20 
-   progress,
21 
-   Rcpp
22 
-Suggests: testthat
19 
+   Rcpp,
20 
+   reshape2,
21 
+   methods,
22 
+   rlang,
23 
+   purrr,
24 
+   Matrix
25 
+Suggests:
26 
+   testthat,
27 
+   readr
23 28 
 RoxygenNote: 6.1.0
24 29 
 LinkingTo: Rcpp
25 30 
 NeedsCompilation: yes
Browse code

more minimal set of FindMyFriends

Andrew McDavid authored on 08/10/2018 02:45:45
Showing 1 changed files
DESCRIPTION
History View file @ 98ae034
... ... 
@@ -5,7 +5,8 @@ Version: 0.1.0
5 5 
 Author: Andrew McDavid
6 6 
 Maintainer: Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
7 7 
 Description: Methods to cluster and analyze high-throughput single cell immune cell repertoires,
8 
-    especially from the 10X Genomics VDJ solution. Tests for specific expansion, as well as omnibus oligoclonality under hypergeometric models.
8 
+    especially from the 10X Genomics VDJ solution.
9 
+    Tests for specific expansion, as well as omnibus oligoclonality under hypergeometric models.
9 10 
 License: GPL-3
10 11 
 Encoding: UTF-8
11 12 
 LazyData: true
Browse code

Initial commit. Extra files from FindMyFriends.

Andrew McDavid authored on 08/10/2018 02:40:14
Showing 1 changed files
DESCRIPTION
History View file @ a1725dd
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,24 @@
1 
+Package: CellaRepertorium
2 
+Type: Package
3 
+Title: Methods for clustering and analyzing high-throughput single cell immune cell repertoires (RepSeq)
4 
+Version: 0.1.0
5 
+Author: Andrew McDavid
6 
+Maintainer: Andrew McDavid <Andrew_McDavid@urmc.rochester.edu>
7 
+Description: Methods to cluster and analyze high-throughput single cell immune cell repertoires,
8 
+    especially from the 10X Genomics VDJ solution. Tests for specific expansion, as well as omnibus oligoclonality under hypergeometric models.
9 
+License: GPL-3
10 
+Encoding: UTF-8
11 
+LazyData: true
12 
+Imports:
13 
+   httr,
14 
+   readr,
15 
+   dplyr,
16 
+   tibble,
17 
+   stringr,
18 
+   Biostrings,
19 
+   progress,
20 
+   Rcpp
21 
+Suggests: testthat
22 
+RoxygenNote: 6.1.0
23 
+LinkingTo: Rcpp
24 
+NeedsCompilation: yes