1. LymphoSeq
  2. DESCRIPTION
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:46:30
Showing 1 changed files
DESCRIPTION
History View file @ bf68fd6
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.28.0
3 
+Version: 1.29.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_17 branch

J Wokaty authored on 25/04/2023 14:46:30
Showing 1 changed files
DESCRIPTION
History View file @ 6173b0b
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.27.0
3 
+Version: 1.28.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

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

J Wokaty authored on 01/11/2022 15:13:34
Showing 1 changed files
DESCRIPTION
History View file @ 7d4ee8c
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.26.0
3 
+Version: 1.27.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
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 15:13:34
Showing 1 changed files
DESCRIPTION
History View file @ 2aa5858
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.25.0
3 
+Version: 1.26.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

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

Nitesh Turaga authored on 26/04/2022 15:31:49
Showing 1 changed files
DESCRIPTION
History View file @ 0a112fa
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.24.0
3 
+Version: 1.25.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
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 15:31:49
Showing 1 changed files
DESCRIPTION
History View file @ 19c829d
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.23.0
3 
+Version: 1.24.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

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

Nitesh Turaga authored on 26/10/2021 16:27:20
Showing 1 changed files
DESCRIPTION
History View file @ 5913728
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.22.0
3 
+Version: 1.23.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
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 16:27:20
Showing 1 changed files
DESCRIPTION
History View file @ c0b2fd4
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.21.0
3 
+Version: 1.22.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

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

Nitesh Turaga authored on 19/05/2021 16:19:57
Showing 1 changed files
DESCRIPTION
History View file @ 0be33e1
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.20.0
3 
+Version: 1.21.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
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 16:19:57
Showing 1 changed files
DESCRIPTION
History View file @ 672762d
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.19.0
3 
+Version: 1.20.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

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

Nitesh Turaga authored on 27/10/2020 15:14:07
Showing 1 changed files
DESCRIPTION
History View file @ 62417bb
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.18.0
3 
+Version: 1.19.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
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 15:14:07
Showing 1 changed files
DESCRIPTION
History View file @ 294dfbb
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.17.0
3 
+Version: 1.18.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:57:02
Showing 1 changed files
DESCRIPTION
History View file @ 0d7d43f
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.16.0
3 
+Version: 1.17.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:57:02
Showing 1 changed files
DESCRIPTION
History View file @ 7b12c51
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.15.0
3 
+Version: 1.16.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:41:00
Showing 1 changed files
DESCRIPTION
History View file @ c3038d7
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.14.0
3 
+Version: 1.15.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:09:37
Showing 1 changed files
DESCRIPTION
History View file @ 4d8ac03
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.13.0
3 
+Version: 1.14.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:13:25
Showing 1 changed files
DESCRIPTION
History View file @ 9b6042d
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.12.0
3 
+Version: 1.13.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:54:01
Showing 1 changed files
DESCRIPTION
History View file @ ba3e8d5
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.11.0
3 
+Version: 1.12.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:36
Showing 1 changed files
DESCRIPTION
History View file @ 04ebe1e
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.10.0
3 
+Version: 1.11.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:42:01
Showing 1 changed files
DESCRIPTION
History View file @ 255c541
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.9.2
3 
+Version: 1.10.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

remove useDevel mentions

LiNk-NY authored on 07/09/2018 18:12:55
Showing 1 changed files
DESCRIPTION
History View file @ 2f2291a
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.9.1
3 
+Version: 1.9.2
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:51:24
Showing 1 changed files
DESCRIPTION
History View file @ be1f085
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.9.0
3 
+Version: 1.9.1
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:42
Showing 1 changed files
DESCRIPTION
History View file @ 8c2a99e
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.8.0
3 
+Version: 1.9.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:41
Showing 1 changed files
DESCRIPTION
History View file @ ec13d7a
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.7.0
3 
+Version: 1.8.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:54:20
Showing 1 changed files
DESCRIPTION
History View file @ e1ffad9
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.6.0
3 
+Version: 1.7.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:41:16
Showing 1 changed files
DESCRIPTION
History View file @ 2b7047a
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.4.1
3 
+Version: 1.6.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

Updated version number

davidcoffey authored on 04/09/2017 17:52:37
Showing 1 changed files
DESCRIPTION
History View file @ d1c5142
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.5.1
3 
+Version: 1.4.1
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

Fixed topSeqsPlot example

davidcoffey authored on 17/05/2017 01:05:37
Showing 1 changed files
DESCRIPTION
History View file @ beaaf51
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.3.1
3 
+Version: 1.5.1
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

Fixed type-os

davidcoffey authored on 14/04/2017 23:00:51
Showing 1 changed files
DESCRIPTION
History View file @ e3b4f74
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.3.0
3 
+Version: 1.3.1
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

Fixed build errors

From: davidcoffey <dcoffey@fredhutch.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq@128255 bc3139a8-67e5-0310-9ffc-ced21a209358

d.coffey authored on 07/04/2017 06:37:57
Showing 1 changed files
DESCRIPTION
History View file @ b158dd3
... ... 
@@ -17,5 +17,5 @@ LazyData: true
17 17 
 RoxygenNote: 6.0.1
18 18 
 Suggests: knitr, pheatmap, wordcloud, rmarkdown
19 19 
 VignetteBuilder: knitr
20 
-biocViews: Software, Technology, Sequencing, TargetedResequencing
20 
+biocViews: Software, Technology, Sequencing, TargetedResequencing, Alignment, MultipleSequenceAlignment
21 21 
 NeedsCompilation: no
Browse code

Fixed build errors

From: davidcoffey <dcoffey@fredhutch.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq@128216 bc3139a8-67e5-0310-9ffc-ced21a209358

d.coffey authored on 06/04/2017 23:57:06
Showing 1 changed files
DESCRIPTION
History View file @ 1cd89da
... ... 
@@ -8,10 +8,10 @@ Description: This R package analyzes high-throughput sequencing of T
8 8 
         sequences generated by Adaptive Biotechnologies' ImmunoSEQ
9 9 
         assay.  Its input comes from tab-separated value (.tsv) files
10 10 
         exported from the ImmunoSEQ analyzer.
11 
-Depends: R (>= 3.2), LymphoSeqDB
11 
+Depends: R (>= 3.3), LymphoSeqDB
12 12 
 Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
13 13 
         RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings,
14 
-        phangorn, doMC, stringdist
14 
+        phangorn, stringdist, UpSetR
15 15 
 License: Artistic-2.0
16 16 
 LazyData: true
17 17 
 RoxygenNote: 6.0.1
Browse code

Added commonSeqsBar function

From: davidcoffey <dcoffey@fredhutch.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq@128214 bc3139a8-67e5-0310-9ffc-ced21a209358

d.coffey authored on 06/04/2017 23:56:53
Showing 1 changed files
DESCRIPTION
History View file @ d915d25
... ... 
@@ -14,7 +14,7 @@ Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
14 14 
         phangorn, doMC, stringdist
15 15 
 License: Artistic-2.0
16 16 
 LazyData: true
17 
-RoxygenNote: 5.0.1
17 
+RoxygenNote: 6.0.1
18 18 
 Suggests: knitr, pheatmap, wordcloud, rmarkdown
19 19 
 VignetteBuilder: knitr
20 20 
 biocViews: Software, Technology, Sequencing, TargetedResequencing
Browse code

Added additional suggests packages

From: davidcoffey <dcoffey@fredhutch.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq@125567 bc3139a8-67e5-0310-9ffc-ced21a209358

d.coffey authored on 03/01/2017 00:58:19
Showing 1 changed files
DESCRIPTION
History View file @ a064323
... ... 
@@ -15,7 +15,7 @@ Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
15 15 
 License: Artistic-2.0
16 16 
 LazyData: true
17 17 
 RoxygenNote: 5.0.1
18 
-Suggests: knitr, pheatmap, wordcloud
18 
+Suggests: knitr, pheatmap, wordcloud, rmarkdown
19 19 
 VignetteBuilder: knitr
20 20 
 biocViews: Software, Technology, Sequencing, TargetedResequencing
21 21 
 NeedsCompilation: no
Browse code

Sync with devel branch

From: davidcoffey <dcoffey@fredhutch.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq@125556 bc3139a8-67e5-0310-9ffc-ced21a209358

d.coffey authored on 02/01/2017 19:15:20
Showing 0 changed files
Browse code

Updated version number

davidcoffey authored on 02/01/2017 18:32:06
Showing 1 changed files
DESCRIPTION
History View file @ 941e3b2
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.1.0
3 
+Version: 1.2.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z versions to odd 'y' after creation of 3_4 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 17/10/2016 19:10:43
Showing 1 changed files
DESCRIPTION
History View file @ 5284e4e
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.2.0
3 
+Version: 1.3.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

bump x.y.z versions to even 'y' prior to creation of 3_4 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

hpages@fhcrc.org authored on 17/10/2016 18:45:06
Showing 1 changed files
DESCRIPTION
History View file @ 834cf4d
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.1.2
3 
+Version: 1.2.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

Added new function clonalRelatedness

davidcoffey authored on 25/05/2016 18:16:05
Showing 1 changed files
DESCRIPTION
History View file @ 2120d15
... ... 
@@ -11,7 +11,7 @@ Description: This R package analyzes high-throughput sequencing of T
11 11 
 Depends: R (>= 3.2), LymphoSeqDB
12 12 
 Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
13 13 
         RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings,
14 
-        phangorn, doMC
14 
+        phangorn, doMC, stringdist
15 15 
 License: Artistic-2.0
16 16 
 LazyData: true
17 17 
 RoxygenNote: 5.0.1
Browse code

Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq@117512 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 15/05/2016 20:14:22
Showing 1 changed files
DESCRIPTION
History View file @ 6de3412
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.1.1
3 
+Version: 1.1.2
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq@117323 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 11/05/2016 23:05:31
Showing 1 changed files
DESCRIPTION
History View file @ bcd324d
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.1.0
3 
+Version: 1.1.1
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

Added functions alignSeq, phyloSeq, exportFasta, differentialAbundance

davidcoffey authored on 10/05/2016 23:14:17
Showing 1 changed files
DESCRIPTION
History View file @ fe27699
... ... 
@@ -10,7 +10,8 @@ Description: This R package analyzes high-throughput sequencing of T
10 10 
         exported from the ImmunoSEQ analyzer.
11 11 
 Depends: R (>= 3.2), LymphoSeqDB
12 12 
 Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
13 
-        RColorBrewer, circlize, grid, utils, stats
13 
+        RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings,
14 
+        phangorn, doMC
14 15 
 License: Artistic-2.0
15 16 
 LazyData: true
16 17 
 RoxygenNote: 5.0.1
Browse code

bump version after creating 3.3 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq@117081 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 03/05/2016 21:30:44
Showing 1 changed files
DESCRIPTION
History View file @ f004b93
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 1.0.0
3 
+Version: 1.1.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

Bump versions prior to creation of 3.3 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq@117079 bc3139a8-67e5-0310-9ffc-ced21a209358

d.tenenbaum authored on 03/05/2016 21:20:18
Showing 1 changed files
DESCRIPTION
History View file @ 648db59
... ... 
@@ -1,6 +1,6 @@
1 1 
 Package: LymphoSeq
2 2 
 Title: Analyze high-throughput sequencing of T and B cell receptors
3 
-Version: 0.99.3
3 
+Version: 1.0.0
4 4 
 Author: David Coffey <dcoffey@fredhutch.org>
5 5 
 Maintainer: David Coffey <dcoffey@fredhutch.org>
6 6 
 Description: This R package analyzes high-throughput sequencing of T
Browse code

Adding pcaExplorer, oppar, pqsfinder, BgeeDB, genbankr, LymphoSeq, pbcmc, InteractionSet, ClusterSignificance

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LymphoSeq@115899 bc3139a8-67e5-0310-9ffc-ced21a209358

mtmorgan@fhcrc.org authored on 06/04/2016 16:10:37
Showing 1 changed files
DESCRIPTION
History View file @ b307a03
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,20 @@
1 
+Package: LymphoSeq
2 
+Title: Analyze high-throughput sequencing of T and B cell receptors
3 
+Version: 0.99.3
4 
+Author: David Coffey <dcoffey@fredhutch.org>
5 
+Maintainer: David Coffey <dcoffey@fredhutch.org>
6 
+Description: This R package analyzes high-throughput sequencing of T
7 
+        and B cell receptor complementarity determining region 3 (CDR3)
8 
+        sequences generated by Adaptive Biotechnologies' ImmunoSEQ
9 
+        assay.  Its input comes from tab-separated value (.tsv) files
10 
+        exported from the ImmunoSEQ analyzer.
11 
+Depends: R (>= 3.2), LymphoSeqDB
12 
+Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
13 
+        RColorBrewer, circlize, grid, utils, stats
14 
+License: Artistic-2.0
15 
+LazyData: true
16 
+RoxygenNote: 5.0.1
17 
+Suggests: knitr, pheatmap, wordcloud
18 
+VignetteBuilder: knitr
19 
+biocViews: Software, Technology, Sequencing, TargetedResequencing
20 
+NeedsCompilation: no