diff --git a/DESCRIPTION b/DESCRIPTION
index 686e7ac..4ea3821 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -40,4 +40,4 @@ biocViews: Sequencing, RNASeq, GeneExpression,
     AlternativeSplicing, SingleCell
 VignetteBuilder: knitr
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
diff --git a/R/alevin-loadFry.R b/R/alevin-loadFry.R
index 72803e2..cbfdcfd 100644
--- a/R/alevin-loadFry.R
+++ b/R/alevin-loadFry.R
@@ -19,10 +19,10 @@
 #' The first column is assumed to be the barcodes and is named as "barcodes".
 #' Extra auxiliary columns in the barcodes file without a specified name will be ignored.
 #' @param gene_id_to_name path to a file that contains the mapping from gene names to gene ids. 
-#' It is only needed if
-#' 1. you are not using the simpleaf pipeline (`simpleaf index` + `simpleaf quant`), \\
-#' 2. you have such a file, and, \\
-#' 3. you want to add this information to the coldata of your anndata. \\
+#' It is only needed if\cr
+#'   1. you are not using the simpleaf pipeline (`simpleaf index` + `simpleaf quant`),\cr
+#'   2. you have such a file, and,\cr
+#'   3. you want to add this information to the colData of your output object.\cr
 #' If you do, please ensure it is a tab-separated, two-column file without a header, and the first column is the gene ids and the second column is the gene names.
 #' @param nonzero whether to filter cells with non-zero expression
 #' value across all genes (default \code{FALSE}).
diff --git a/man/fishpond-package.Rd b/man/fishpond-package.Rd
index 3254b58..ba5bbac 100644
--- a/man/fishpond-package.Rd
+++ b/man/fishpond-package.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/fishpond.R
 \docType{package}
 \name{fishpond-package}
+\alias{fishpond}
 \alias{fishpond-package}
 \title{Fishpond: downstream methods and tools for expression data}
 \description{
@@ -46,5 +47,38 @@ Patro, R., Love, M.I. (2020)
 Compression of quantification uncertainty for scRNA-seq counts.
 bioRxiv.
 \url{https://doi.org/10.1101/2020.07.06.189639}
+}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://thelovelab.github.io/fishpond}
+  \item \url{https://thelovelab.com/mikelove/fishpond}
+  \item Report bugs at \url{https://support.bioconductor.org/tag/fishpond}
+}
+
+}
+\author{
+\strong{Maintainer}: Michael Love \email{michaelisaiahlove@gmail.com}
+
+Authors:
+\itemize{
+  \item Anqi Zhu [contributor]
+  \item Avi Srivastava [contributor]
+  \item Rob Patro [contributor]
+  \item Joseph Ibrahim [contributor]
+}
+
+Other contributors:
+\itemize{
+  \item Hirak Sarkar [contributor]
+  \item Euphy Wu [contributor]
+  \item Noor Pratap Singh [contributor]
+  \item Scott Van Buren [contributor]
+  \item Dongze He [contributor]
+  \item Steve Lianoglou [contributor]
+  \item Wes Wilson [contributor]
+  \item Jeroen Gilis [contributor]
+}
+
 }
 \keyword{package}
diff --git a/man/loadFry.Rd b/man/loadFry.Rd
index 815b372..abccbe0 100644
--- a/man/loadFry.Rd
+++ b/man/loadFry.Rd
@@ -4,7 +4,14 @@
 \alias{loadFry}
 \title{Load in data from alevin-fry USA mode}
 \usage{
-loadFry(fryDir, outputFormat = "scRNA", nonzero = FALSE, quiet = FALSE)
+loadFry(
+  fryDir,
+  outputFormat = "scRNA",
+  aux_columns = c("X", "Y"),
+  gene_id_to_name = NULL,
+  nonzero = FALSE,
+  quiet = FALSE
+)
 }
 \arguments{
 \item{fryDir}{path to the output directory returned by
@@ -16,10 +23,22 @@ alevin-fry quant command. This directory should contain a
 \item{outputFormat}{can be \emph{either} be a list that defines the
 desired format of the output \code{SingleCellExperiment} object
 \emph{or} a string that represents one of the pre-defined output
-formats, which are "scRNA", "snRNA", "all", "scVelo", "velocity", "U+S+A" and "S+A".
+formats, which are "scRNA" (or "S+A"), "snRNA" (or "all", "U+S+A"), "scVelo", and "velocity".
 See details for the explanations of the pre-defined formats and
 how to define custom format.}
 
+\item{aux_columns}{vector of characters containing the column names of the
+auxiliary information in the barcodes file starting from the second column.
+The first column is assumed to be the barcodes and is named as "barcodes".
+Extra auxiliary columns in the barcodes file without a specified name will be ignored.}
+
+\item{gene_id_to_name}{path to a file that contains the mapping from gene names to gene ids. 
+It is only needed if\cr
+  1. you are not using the simpleaf pipeline (`simpleaf index` + `simpleaf quant`),\cr
+  2. you have such a file, and,\cr
+  3. you want to add this information to the colData of your output object.\cr
+If you do, please ensure it is a tab-separated, two-column file without a header, and the first column is the gene ids and the second column is the gene names.}
+
 \item{nonzero}{whether to filter cells with non-zero expression
 value across all genes (default \code{FALSE}).
 If \code{TRUE}, this will filter based on all assays.