diff --git a/man/ScanVcfParam-class.Rd b/man/ScanVcfParam-class.Rd
index e49683a..098005b 100644
--- a/man/ScanVcfParam-class.Rd
+++ b/man/ScanVcfParam-class.Rd
@@ -74,10 +74,10 @@
   \item{trimEmpty}{A logical(1) indicating whether \sQuote{GENO} fields
     with no values should be returned.
   }
-  \item{which}{A \code{\linkS4class{GRanges}} describing the sequences and
-    ranges to be queried. Variants whose \code{POS} lies in the interval(s)
-    \code{[start, end]} are returned. If \code{which} is not specified all
-    ranges are returned. 
+  \item{which}{A \link[GenomicRanges:GRanges-class]{GRanges} describing the
+    sequences and ranges to be queried. Variants whose \code{POS} lies in the
+    interval(s) \code{[start, end]} are returned. If \code{which} is not
+    specified all ranges are returned.
   }
   \item{object}{An instance of class \code{ScanVcfParam}.
   }
diff --git a/man/VCF-class.Rd b/man/VCF-class.Rd
index b3320bc..efb8343 100644
--- a/man/VCF-class.Rd
+++ b/man/VCF-class.Rd
@@ -315,7 +315,7 @@
   This function converts the output from the \link[snpStats]{read.plink} 
   function to a \code{VCF} class. \code{from} must be a list of length 3
   with named elements "map", "fam" and "genotypes". \code{seqSource} can
-  be a \code{\link[BSgenome]{BSgenome}} or an \link{FaFile}
+  be a \code{\link[BSgenome]{BSgenome}} or an \link[Rsamtools]{FaFile}
   used for reference sequence extraction.
 }
 
@@ -376,23 +376,23 @@
 
   Slots unique to \code{VCF} and subclasses,
   \itemize{
-    \item \code{fixed}: A \link{DataFrame} containing the REF, ALT, QUAL 
-      and FILTER fields from a VCF file.
-    \item \code{info}: A \link{DataFrame} containing the INFO fields from 
-      a VCF file.
+    \item \code{fixed}: A \link[S4Vectors:DataFrame-class]{DataFrame} containing
+      the REF, ALT, QUAL  and FILTER fields from a VCF file.
+    \item \code{info}: A \link[S4Vectors:DataFrame-class]{DataFrame} containing
+      the INFO fields from  a VCF file.
   }
 
   Slots inherited from \code{RangedSummarizedExperiment},
   \itemize{
     \item \code{metadata}: A \code{list} containing the 
           file header or other information about the overall experiment.
-    \item \code{rowRanges}: A \link{GRanges}-class instance defining the
-           variant ranges and associated metadata columns of REF, ALT, QUAL 
-           and FILTER. While the REF, ALT, QUAL and FILTER fields can
-           be displayed as metadata columns they cannot be modified with
-           \code{rowRanges<-}. To modify these fields use \code{fixed<-}. 
-    \item \code{colData}: A \link{DataFrame}-class instance describing the 
-          samples and associated metadata.
+    \item \code{rowRanges}: A \link[GenomicRanges:GRanges-class]{GRanges} class
+           instance defining the variant ranges and associated metadata columns
+           of REF, ALT, QUAL and FILTER. While the REF, ALT, QUAL and FILTER
+           fields can be displayed as metadata columns they cannot be modified
+           with \code{rowRanges<-}. To modify these fields use \code{fixed<-}.
+    \item \code{colData}: A \link[S4Vectors:DataFrame-class]{DataFrame} class
+          instance describing the samples and associated metadata.
     \item \code{geno}: The \code{assays} slot from
           \code{RangedSummarizedExperiment} has been renamed as \code{geno}
           for the VCF class. This slot contains the genotype information
@@ -413,7 +413,7 @@
 \author{Valerie Obenchain}
 
 \seealso{
-  \link{GRanges},
+  \link[GenomicRanges:GRanges-class]{GRanges},
   \link[S4Vectors]{DataFrame},
   \link[S4Vectors]{SimpleList},
   \link[SummarizedExperiment]{RangedSummarizedExperiment},
diff --git a/man/VCFHeader-class.Rd b/man/VCFHeader-class.Rd
index 51d20c7..622b0d8 100644
--- a/man/VCFHeader-class.Rd
+++ b/man/VCFHeader-class.Rd
@@ -143,7 +143,7 @@
     }
     \item{\code{sample}}{character() vector 
     }
-    \item{\code{header}}{\link{DataFrameList}-class
+    \item{\code{header}}{\link[IRanges:DataFrameList-class]{DataFrameList} class
     }
   }
 }
@@ -152,7 +152,7 @@
 
 \seealso{
   \code{\link{scanVcfHeader}},
-  \code{\link{DataFrameList}}
+  \code{\link[IRanges:DataFrameList-class]{DataFrameList}}
 }
 
 \examples{
diff --git a/man/VcfFile-class.Rd b/man/VcfFile-class.Rd
index 3523680..65d8406 100644
--- a/man/VcfFile-class.Rd
+++ b/man/VcfFile-class.Rd
@@ -99,14 +99,15 @@
 \section{Fields}{
 
   \code{VcfFile} and \code{VcfFileList} classes inherit fields from the
-  \code{\linkS4class{TabixFile}} and \code{\linkS4class{TabixFileList}} 
+  \code{\link[Rsamtools]{TabixFile}} and \code{\link[Rsamtools]{TabixFileList}}
   classes.
 }
 
 \section{Functions and methods}{
 
   \code{VcfFile} and \code{VcfFileList} classes inherit methods from the
-  \code{\linkS4class{TabixFile}} and \code{\linkS4class{TabixFileList}} 
+  \code{\link[Rsamtools:TabixFile-class]{TabixFile}} and
+  \code{\link[Rsamtools:TabixFileList-class]{TabixFileList}}
   classes.
 
   ## Opening / closing:
diff --git a/man/defunct.Rd b/man/defunct.Rd
index 3161db8..4779b35 100644
--- a/man/defunct.Rd
+++ b/man/defunct.Rd
@@ -79,7 +79,7 @@
 
 \seealso{
   \itemize{
-    \item \code{\link{expand}}
+    \item \code{\link[S4Vectors]{expand}}
     \item \code{\link{filterVcf}}
     \item \code{\link{genotypeToSnpMatrix}}
     \item \code{\link[GenomicFeatures]{mapToTranscripts}}
diff --git a/man/filterVcf-methods.Rd b/man/filterVcf-methods.Rd
index 498c3f8..5368a19 100644
--- a/man/filterVcf-methods.Rd
+++ b/man/filterVcf-methods.Rd
@@ -20,7 +20,7 @@
 }
 
 \arguments{
-  \item{file}{A \code{character(1)} file path or \code{\link{TabixFile}}
+  \item{file}{A \code{character(1)} file path or \code{\link[Rsamtools]{TabixFile}}
     specifying the VCF file to be filtered.}
 
   \item{genome}{A \code{character(1)} identifier}
@@ -34,14 +34,14 @@
     messages should be printed.}
 
   \item{index}{A \code{logical(1)} indicating whether the filtered file
-    should be compressed and indexed (using \code{\link{bgzip}} and
-    \code{indexTabix}).}
+    should be compressed and indexed (using \code{\link[Rsamtools]{bgzip}} and
+    \code{\link[Rsamtools]{indexTabix}}).}
 
-  \item{prefilters}{A \code{\link{FilterRules}} instance contains rules for
-    filtering un-parsed lines of the VCF file.}
+  \item{prefilters}{A \code{\link[S4Vectors:FilterRules-class]{FilterRules}}
+    instance contains rules for filtering un-parsed lines of the VCF file.}
 
-  \item{filters}{A \code{\link{FilterRules}} instance contains rules for
-    filtering fully parsed VCF objects.}
+  \item{filters}{A \code{\link[S4Vectors:FilterRules-class]{FilterRules}}
+    instance contains rules for filtering fully parsed VCF objects.}
 
   \item{param}{A \code{\link{ScanVcfParam}} instance restricting input
     of particular \code{info} or \code{geno} fields, or genomic
diff --git a/man/indexVcf-method.Rd b/man/indexVcf-method.Rd
index 2282ae8..e0f8078 100644
--- a/man/indexVcf-method.Rd
+++ b/man/indexVcf-method.Rd
@@ -31,7 +31,7 @@
 \details{
   If \code{x} is a character vector, assumes they are the path(s) to
   bgzf-compressed VCF file(s). If an index does not exist, one is
-  created. VCF files can be compreseed using \code{\link{bgzip}}. A
+  created. VCF files can be compreseed using \code{\link[Rsamtools]{bgzip}}. A
   \code{VcfFile} or \code{VcfFileList} is returned.
 
   If a \code{VcfFile} or \code{VcfFileList} is given, the index file is
diff --git a/man/predictCoding-methods.Rd b/man/predictCoding-methods.Rd
index 6bbe61c..f1aecf7 100644
--- a/man/predictCoding-methods.Rd
+++ b/man/predictCoding-methods.Rd
@@ -21,12 +21,13 @@
 }
 
 \arguments{
-  \item{query}{A \linkS4class{VCF}, \link{IntegerRanges}, \link{GRanges} or
-    \code{VRanges} instance containing the variants to be annotated. If
-    \code{query} is a \link[IRanges]{IntegerRanges} or \code{VRanges} it is
-    coerced to a \link{GRanges}.  If a \linkS4class{VCF} is provided the
-    \code{GRanges} returned by the \code{rowRanges()} accessor will be used.
-    All metadata columns are ignored.
+  \item{query}{A \linkS4class{VCF}, \link[IRanges]{IntegerRanges},
+    \link[GenomicRanges:GRanges-class]{GRanges} or \code{VRanges} instance
+    containing the variants to be annotated. If \code{query} is a
+    \link[IRanges]{IntegerRanges} or \code{VRanges} it is coerced to a
+    \link[GenomicRanges:GRanges-class]{GRanges}.  If a \linkS4class{VCF} is
+    provided the \code{GRanges} returned by the \code{rowRanges()} accessor will
+    be used. All metadata columns are ignored.
 
     When \code{query} is not a \code{VCF} object a \code{varAllele} must be
     provided. The \code{varAllele} must be a \code{DNAStringSet} the same length
@@ -43,8 +44,8 @@
     \link[GenomicFeatures]{TxDb} objects with 
     \code{makeTxDbFromGFF()} in the \code{txdbmaker} package.
   } 
-  \item{seqSource}{A \code{\link[BSgenome]{BSgenome}} instance or an \link{FaFile}
-    to be used for sequence extraction.
+  \item{seqSource}{A \code{\link[BSgenome]{BSgenome}} instance or an
+    \link[Rsamtools]{FaFile} to be used for sequence extraction.
   }
   \item{varAllele}{A \link[Biostrings]{DNAStringSet} containing the variant
     (alternate) alleles. The length of \code{varAllele} must equal the length
diff --git a/man/readVcf-methods.Rd b/man/readVcf-methods.Rd
index 6ed0af3..2058d65 100644
--- a/man/readVcf-methods.Rd
+++ b/man/readVcf-methods.Rd
@@ -51,7 +51,7 @@ readGT(file, nucleotides=FALSE, param=ScanVcfParam(), ..., row.names=TRUE)
 
 \arguments{
   \item{file}{A \code{\link{VcfFile}} (synonymous with
-    \code{\link{TabixFile}}) instance or character() name of the VCF
+    \code{\link[Rsamtools]{TabixFile}}) instance or character() name of the VCF
     file to be processed. When ranges are specified in \code{param},
     \code{file} must be a \code{\link{VcfFile}}.
 
@@ -268,10 +268,10 @@ readGT(file, nucleotides=FALSE, param=ScanVcfParam(), ..., row.names=TRUE)
 \seealso{
   \code{\link{indexVcf}},
   \code{\link{VcfFile}},
-  \code{\link{indexTabix}},
-  \code{\link{TabixFile}},
-  \code{\link{scanTabix}},
-  \code{\link{scanBcf}},
+  \code{\link[Rsamtools]{indexTabix}},
+  \code{\link[Rsamtools]{TabixFile}},
+  \code{\link[Rsamtools]{scanTabix}},
+  \code{\link[Rsamtools]{scanBcf}},
   \code{\link{expand,CollapsedVCF-method}}
 }
 
diff --git a/man/scanVcf-methods.Rd b/man/scanVcf-methods.Rd
index a1a92a9..94f9fba 100644
--- a/man/scanVcf-methods.Rd
+++ b/man/scanVcf-methods.Rd
@@ -41,7 +41,7 @@ scanVcf(file, ..., param)
 
 \arguments{
   \item{file}{For \code{scanVcf} and \code{scanVcfHeader}, the character() 
-    file name, \code{\link{TabixFile}}, or class \code{connection} 
+    file name, \code{\link[Rsamtools]{TabixFile}}, or class \code{connection}
     (\code{file()} or \code{bgzip()}) of the \sQuote{VCF} file to be 
     processed.
   }
@@ -56,7 +56,7 @@ scanVcf(file, ..., param)
 \details{
   The argument \code{param} allows portions of the file to be input, but 
   requires that the file be bgzip'd and indexed as a 
-  \code{\linkS4class{TabixFile}}.
+  \code{\link[Rsamtools]{TabixFile}}.
 
   \code{scanVcf} with \code{param="missing"} and \code{file="character"}
   or \code{file="connection"} scan the entire file. With
@@ -134,8 +134,8 @@ scanVcf(file, ..., param)
 
 \seealso{
   \code{\link{readVcf}} 
-  \code{\link{BcfFile}} 
-  \code{\link{TabixFile}}
+  \code{\link[Rsamtools]{BcfFile}}
+  \code{\link[Rsamtools]{TabixFile}}
 }
 
 \author{