hansenlab · kasperdanielhansen · Aug 18, 2026 · Aug 17, 2026 · Aug 17, 2026 · Aug 17, 2026
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: bsseq
-Version: 1.47.6
+Version: 1.47.7
 Encoding: UTF-8
 Title: Analyze, manage and store whole-genome methylation data
 Description: A collection of tools for analyzing and visualizing whole-genome
@@ -52,7 +52,8 @@ Suggests:
     doParallel,
     rtracklayer,
     BSgenome.Hsapiens.UCSC.hg38,
-    batchtools
+    batchtools,
+    tidyverse
 Collate:
     utils.R
     hasGRanges.R

diff --git a/inst/extdata/longread/silversides/all_cpgs/AA1.bedmethyl.gz b/inst/extdata/longread/silversides/all_cpgs/AA1.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/all_cpgs/AA2.bedmethyl.gz b/inst/extdata/longread/silversides/all_cpgs/AA2.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/all_cpgs/AA3.bedmethyl.gz b/inst/extdata/longread/silversides/all_cpgs/AA3.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/all_cpgs/AR1.bedmethyl.gz b/inst/extdata/longread/silversides/all_cpgs/AR1.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/all_cpgs/AR2.bedmethyl.gz b/inst/extdata/longread/silversides/all_cpgs/AR2.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/all_cpgs/AR3.bedmethyl.gz b/inst/extdata/longread/silversides/all_cpgs/AR3.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/all_cpgs/RR1.bedmethyl.gz b/inst/extdata/longread/silversides/all_cpgs/RR1.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/all_cpgs/RR2.bedmethyl.gz b/inst/extdata/longread/silversides/all_cpgs/RR2.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/all_cpgs/RR3.bedmethyl.gz b/inst/extdata/longread/silversides/all_cpgs/RR3.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/mc_filtered.hdf5/assays.h5 b/inst/extdata/longread/silversides/mc_filtered.hdf5/assays.h5
diff --git a/inst/extdata/longread/silversides/mc_filtered.hdf5/se.rds b/inst/extdata/longread/silversides/mc_filtered.hdf5/se.rds
diff --git a/inst/extdata/longread/silversides/ref_cpgs/AA1.bedmethyl.gz b/inst/extdata/longread/silversides/ref_cpgs/AA1.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/ref_cpgs/AA2.bedmethyl.gz b/inst/extdata/longread/silversides/ref_cpgs/AA2.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/ref_cpgs/AA3.bedmethyl.gz b/inst/extdata/longread/silversides/ref_cpgs/AA3.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/ref_cpgs/AR1.bedmethyl.gz b/inst/extdata/longread/silversides/ref_cpgs/AR1.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/ref_cpgs/AR2.bedmethyl.gz b/inst/extdata/longread/silversides/ref_cpgs/AR2.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/ref_cpgs/AR3.bedmethyl.gz b/inst/extdata/longread/silversides/ref_cpgs/AR3.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/ref_cpgs/RR1.bedmethyl.gz b/inst/extdata/longread/silversides/ref_cpgs/RR1.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/ref_cpgs/RR2.bedmethyl.gz b/inst/extdata/longread/silversides/ref_cpgs/RR2.bedmethyl.gz
diff --git a/inst/extdata/longread/silversides/ref_cpgs/RR3.bedmethyl.gz b/inst/extdata/longread/silversides/ref_cpgs/RR3.bedmethyl.gz
diff --git a/vignettes/Longread_guide.Rmd b/vignettes/Longread_guide.Rmd
diff --git a/vignettes/bsseq.Rmd b/vignettes/bsseq.Rmd
@@ -156,7 +156,7 @@ from chromosome 22.
 `combine()` combines two `BSseq` objects in the following way: the samples for the return objects is the union of the samples from the two objects, and the methylation loci are the union of the two methylation loci.  The two objects do not need to have measured the same loci (in the example below, `BStmp` has data on chromosome 1 and X).
 
 ```{r data-combine}
-BStmp2 <- combine(BStmp, BS.chr22[1:3,])
+BStmp2 <- bsseq::combine(BStmp, BS.chr22[1:3,])
 granges(BStmp2)
 getCoverage(BStmp2)
 ```