diff --git a/NAMESPACE b/NAMESPACE
index d1e4584..6f4ffe7 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,24 @@
 # Generated by roxygen2: do not edit by hand
 
+export(cytoexperiment)
+export(gate_tail)
+export(gate_tautstring)
+export(gs_to_sce)
+export(gsexperiment)
+export(gslist_clone)
+export(gstreeexperiment)
+export(print.logicle)
+export(readFCSPar)
+export(sce_to_gs)
+export(tailgate)
+export(tautString)
+export(tautStringGate)
+export(tautstring)
+export(tmix2DGate)
+exportClasses(cytoexperiment)
+exportClasses(gsexperiment)
+exportMethods(densityplot)
+exportMethods(keyword)
 import(data.table)
 import(flowCore)
 import(flowWorkspace)
diff --git a/R/tautString.R b/R/tautString.R
index b9b2548..d191769 100644
--- a/R/tautString.R
+++ b/R/tautString.R
@@ -78,10 +78,6 @@ gate_tautstring <- function(fr, channel, gate_range = NULL, min = NULL, max = NU
   }
   return(filters)
 }
-#' @templateVar old tautStringGate
-#' @templateVar new gate_tautstring
-#' @template template-depr_pkg
-NULL
 
 #'@export
 tautStringGate <- function(fr, channel, gate_range = NULL, min = NULL, max = NULL, filterId = ""){
diff --git a/man/densityplot-GatingHierarchy-character-method.Rd b/man/densityplot-GatingHierarchy-character-method.Rd
index 78cadb4..74e1400 100644
--- a/man/densityplot-GatingHierarchy-character-method.Rd
+++ b/man/densityplot-GatingHierarchy-character-method.Rd
@@ -1,6 +1,5 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/densityplot.R
-\docType{methods}
 \name{densityplot,GatingHierarchy,character-method}
 \alias{densityplot,GatingHierarchy,character-method}
 \title{plot the population as densityplot for the channels associated with the gate}
diff --git a/man/gate_tail.Rd b/man/gate_tail.Rd
new file mode 100644
index 0000000..bd17980
--- /dev/null
+++ b/man/gate_tail.Rd
@@ -0,0 +1,158 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tailgate.R
+\name{gate_tail}
+\alias{gate_tail}
+\alias{tailgate}
+\alias{cytokine}
+\alias{.cytokine_cutpoint}
+\title{Gates the tail of a density using the derivative of a kernel density estimate}
+\usage{
+gate_tail(
+  fr,
+  channel,
+  filterId = "",
+  num_peaks = 1,
+  ref_peak = 1,
+  strict = TRUE,
+  tol = 0.01,
+  side = "right",
+  min = NULL,
+  max = NULL,
+  bias = 0,
+  positive = TRUE,
+  ...
+)
+
+.cytokine_cutpoint(
+  x,
+  num_peaks = 1,
+  ref_peak = 1,
+  method = c("first_deriv", "second_deriv"),
+  tol = 0.01,
+  adjust = 1,
+  side = "right",
+  strict = TRUE,
+  plot = FALSE,
+  auto_tol = FALSE,
+  ...
+)
+}
+\arguments{
+\item{fr}{a \code{flowFrame} object}
+
+\item{channel}{the channel from which the cytokine gate is constructed}
+
+\item{filterId}{the name of the filter}
+
+\item{num_peaks}{the number of peaks expected to see. This effectively removes
+any peaks that are artifacts of smoothing}
+
+\item{ref_peak}{After \code{num_peaks} are found, this argument provides the
+index of the reference population from which a gate will be obtained. By
+default, the peak farthest to the left is used.}
+
+\item{strict}{\code{logical} when the actual number of peaks detected is less than \code{ref_peak}. 
+an error is reported by default. But if \code{strict} is set to FALSE, then the reference peak will be reset to the peak of the far right.}
+
+\item{tol}{the tolerance value}
+
+\item{side}{On which side of the density do we want to gate the tail. Valid options are "left" or "right".}
+
+\item{min}{a numeric value that sets the lower boundary for data filtering}
+
+\item{max}{a numeric value that sets the upper boundary for data filtering}
+
+\item{bias}{a numeric value that adds a constant to the calculated cutpoint(threshold). Default is 0.}
+
+\item{positive}{If FALSE, after finding the cutpoint, the \code{rectangleGate} returned will have bounds \code{(-Inf, a]} as opposed to \code{[a, Inf)}.
+This argument will be ignored if \code{gate_tail} is used in a \code{\link{gatingTemplate}} with \code{\link{gt_gating}} or via \code{\link{gs_add_gating_method}}. 
+In those cases, pop = "-" should be used instead.}
+
+\item{...}{additional arguments passed to \code{.deriv_density}}
+
+\item{x}{a \code{numeric} vector used as input data}
+
+\item{method}{the method used to select the cutpoint. See details.}
+
+\item{adjust}{the scaling adjustment applied to the bandwidth used in the
+first derivative of the kernel density estimate}
+
+\item{plot}{logical specifying whether to plot the peaks found
+\code{'right'} (default) or \code{'left'}?}
+
+\item{auto_tol}{when TRUE, it tries to set the tolerance automatically.}
+}
+\value{
+a \code{filterList} containing the gates (cutpoints) for each sample with
+the corresponding \code{\linkS4class{rectangleGate}} objects defining the tail as the positive population.
+
+the cutpoint along the x-axis
+}
+\description{
+These methods aim to set a one-dimensional gate (cutpoint) near the edge of a peak in 
+the density specified by a channel of a \code{\linkS4class{flowFrame}} to isolate the tail population. 
+They allow two approaches to do this, both beginning by obtaining a
+smoothened kernel density estimate (KDE) of the original density and then utilizing either
+its first or second derivative.
+
+We determine a gating cutpoint using either the first or second derivative of
+the kernel density estimate (KDE) of the \code{x}.
+}
+\details{
+The default behavior of the first approach, specified by \code{method = "first_deriv"}, 
+finds valleys in the first derivative of the KDE and uses the lowest such valley
+to place the cutpoint on the steep right shoulder of the largest peak in the original density. 
+
+The default behavior of the second approach, specified by \code{method = "second_deriv"},
+is to find peaks in the second derivative of the KDE and use the largest such peak
+to place the cutpoint at the point on the right shoulder of the largest
+peak in the original density where it is most rapidly flattening (the first derivative is rapidly
+growing less negative).
+
+Both approaches can be significantly modified from defaults with a number of optional
+arguments. The \code{num_peaks} argument specifes how many peaks should be found 
+in the smoothened KDE and \code{ref_peak} specifies around which peak the gate's 
+cutpoint should be placed (starting from the leftmost peak). Setting the \code{side}
+argument to "left" modifies the procedure to put the cutpoint on the left side of the 
+reference peak to isolate a left tail. The \code{max} and \code{min} arguments allow for 
+pre-filtering extreme values in the channel of interest (keeping only observations with 
+channel values less than max and/or more than min). The bandwidth used for kernel density
+estimation can be proportionally scaled using \code{adjust} (e.g. \code{adjust = 0.5} will
+use a bandwidth that is half of the default). This allows for tuning the level of
+smoothing applied in the estimation.
+
+Lastly, the \code{tol}, \code{auto_tol}, and \code{bias} arguments allow for adjustments
+to be made to the cutpoint that would otherwise be returned. \code{tol} provides a tolerance value
+that the absolute value of the KDE derivative at the cutpoint must be under. If the derivative 
+at the original cutpoint is greater than \code{tol} in magnitude, the returned cutpoint will be the first point 
+to the right of the original cutpoint (or to the left in the case of \code{side = "left"}) with corresponding 
+derivative within \code{tol}. Thus in practice, a smaller value for \code{tol} effectively pushes the cutpoint
+further down the shoulder of the peak towards the flat tail. \code{tol} is set to 0.01 by default
+but setting \code{auto_tol = TRUE} will set the tolerance to a reasonable estimate of 
+1\% of the maximum absolute value of the first derivative of the KDE. \code{tol} and
+\code{auto_tol} are only used for \code{method = "first_deriv"}. Additionally, the \code{bias}
+argument allows for directly shifting the returned cutpoint left or right.
+
+It is also possible to pass additional arguments to control the calculation
+of the derivative, which will have some effect on the resulting cutpoint determination,
+but this should usually not be needed. By default the number of grid points for the derivative
+calculation will be 10,000, but this can be changed with \code{num_points}. The default
+bandwidth can also be directly adjusted with \code{bandwidth}, where the final value used
+will be given by \code{adjust*bandwidth}
+
+By default, we compute the first derivative of the kernel density estimate. 
+Next, we determine the lowest valley from the derivative, which corresponds to the
+density's mode for cytokines. We then contruct a gating cutpoint as the value
+less than the tolerance value \code{tol} in magnitude and is also greater
+than the lowest valley.
+
+Alternatively, if the \code{method} is selected as \code{second_deriv}, we
+select a cutpoint from the second derivative of the KDE. Specifically, we
+choose the cutpoint as the largest peak of the second derivative of the KDE
+density which is greater than the reference peak.
+}
+\examples{
+\dontrun{
+ gate <- gate_tail(fr, Channel = "APC-A") # fr is a flowFrame
+}
+}
diff --git a/man/gate_tautstring.Rd b/man/gate_tautstring.Rd
new file mode 100644
index 0000000..17491b5
--- /dev/null
+++ b/man/gate_tautstring.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tautString.R
+\name{tautstring}
+\alias{tautstring}
+\alias{tautString}
+\alias{gate_tautstring}
+\alias{tautStringGate}
+\title{Taut String Density Estimator Gating}
+\usage{
+tautstring(sorted_vector, modeprior = 0)
+
+gate_tautstring(
+  fr,
+  channel,
+  gate_range = NULL,
+  min = NULL,
+  max = NULL,
+  filterId = ""
+)
+}
+\arguments{
+\item{sorted_vector}{\code{numeric} vector of single cell expresion from a single cytometric channel.}
+
+\item{modeprior}{\code{numeric} scalar specifying the expected number of modes. Default 0 (autodetect). Rarely should this be
+set by the user.}
+
+\item{fr}{a flowFrame object}
+
+\item{channel}{The channel to gate.}
+
+\item{gate_range}{The range to look for a gate, no truncation occurs.}
+
+\item{min}{The min range of the data to truncate the flowFrame}
+
+\item{max}{The max range of the data to truncate the flowFrame}
+
+\item{filterId}{The id / name of the gate.}
+}
+\description{
+The taut string density estimator gating returns 0, 1, or more gates, depending on how many modes it identifies in the data.
+}
diff --git a/man/clone-GatingSetList-method.Rd b/man/gslist_clone.Rd
similarity index 62%
rename from man/clone-GatingSetList-method.Rd
rename to man/gslist_clone.Rd
index b05f28f..51d0935 100644
--- a/man/clone-GatingSetList-method.Rd
+++ b/man/gslist_clone.Rd
@@ -1,16 +1,15 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/clone.GatingSetList.R
-\docType{methods}
-\name{clone,GatingSetList-method}
-\alias{clone,GatingSetList-method}
+\name{gslist_clone}
+\alias{gslist_clone}
 \title{clone a GatingSetList}
 \usage{
-\S4method{clone}{GatingSetList}(x, ...)
+gslist_clone(x, ...)
 }
 \arguments{
 \item{x}{A \code{GatingSetList}}
 
-\item{...}{see \code{\link{clone,GatingSet-method}}}
+\item{...}{see \code{\link{gs_clone}}}
 }
 \value{
 A copy of a given \code{GatingSetList}.
@@ -20,7 +19,7 @@ A wrapper that invokes clone method for each underlying GatingSet.
 }
 \examples{
   \dontrun{
-    gslist1<-clone(gslist)
+    gslist1<-gslist_clone(gslist)
 
   }
 }
diff --git a/man/getKeywords-GatingSet-character-method.Rd b/man/keyword-GatingSet-character-method.Rd
similarity index 73%
rename from man/getKeywords-GatingSet-character-method.Rd
rename to man/keyword-GatingSet-character-method.Rd
index 6a97fad..51f9288 100644
--- a/man/getKeywords-GatingSet-character-method.Rd
+++ b/man/keyword-GatingSet-character-method.Rd
@@ -1,11 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/getKeywords.R
-\docType{methods}
-\name{getKeywords,GatingSet,character-method}
-\alias{getKeywords,GatingSet,character-method}
+\name{keyword,GatingSet,character-method}
+\alias{keyword,GatingSet,character-method}
 \title{Fetch a list of keywords from a GatingSet}
 \usage{
-\S4method{getKeywords}{GatingSet,character}(obj, y)
+\S4method{keyword}{GatingSet,character}(object, keyword)
 }
 \arguments{
 \item{obj}{GatingSet}
@@ -21,5 +20,5 @@ No error checking at the moment.
 library(flowWorkspace)
 dataDir <- system.file("extdata",package="flowWorkspaceData")
 suppressMessages(gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE)))
-getKeywords(gs, c("TUBE NAME", "EXPERIMENT NAME"))
+keyword(gs, c("TUBE NAME", "EXPERIMENT NAME"))
 }
diff --git a/man/sce_to_gs.Rd b/man/sce_to_gs.Rd
new file mode 100644
index 0000000..383803b
--- /dev/null
+++ b/man/sce_to_gs.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gsexperiment.R
+\name{sce_to_gs}
+\alias{sce_to_gs}
+\title{convert SingleCellExperiment to a GatingSet}
+\usage{
+sce_to_gs(
+  sce,
+  assay_type = "intensity",
+  sample = "sample",
+  channel = NA,
+  marker = NA,
+  ...
+)
+}
+\arguments{
+\item{sce}{SingleCellExperiment object}
+
+\item{assay_type}{select assay to use}
+
+\item{sample}{select the column from colData to represent sample ID}
+
+\item{channel}{select the column from rowData to represent channels}
+
+\item{marker}{select the column from rowData to represent markers}
+}
+\description{
+note that only selected assay and rowData columns will be extracted into the GatingSet
+}