diff --git a/man/build_count_matrices.Rd b/man/build_count_matrices.Rd
index 0f7a019e21707d0090cbcf3050e9eb0ddedbf3c5..2b863bb9a5456db96ccd263d366e881c50aab903 100644
--- a/man/build_count_matrices.Rd
+++ b/man/build_count_matrices.Rd
@@ -5,28 +5,34 @@
 \title{Build matrices}
 \usage{
 build_count_matrices(
-  design,
+  design_table,
   path,
-  formula,
-  filter_file,
+  my_formula,
+  filter_list,
   min_expression,
   output_folder
 )
 }
 \arguments{
-\item{design}{A design file with the column count_files, sample and condition}
+\item{design_table}{A dataframe with the column count_files, sample and
+condition. Other columns corresponding to cofactors can be present}
 
 \item{path}{The path were the count file are stored}
 
-\item{formula}{The formula to use in DESeq2}
+\item{my_formula}{The formula to use in DESeq2}
 
-\item{filter_file}{A file containing genes}
+\item{filter_list}{A vector containing the list of genes to keep in the
+analysis. To keep all gene use a NULL object}
 
 \item{min_expression}{The minimum average required expression across
 all samples to keep the gene}
 
 \item{output_folder}{Folder were the matrices will be produced}
 }
+\value{
+The dds object corresponding to a DESeqDatase object obtained after
+running the DESeq function.
+}
 \description{
 Build matrices
 }
diff --git a/man/cli_run_deseq2.Rd b/man/cli_run_deseq2.Rd
index 401056b8917b63ce7d6266aedeb28a821468de91..8cef8041107bf6bd15975c1785df868317720cc4 100644
--- a/man/cli_run_deseq2.Rd
+++ b/man/cli_run_deseq2.Rd
@@ -16,6 +16,6 @@ perform a complete DESeq2 analysis including:
 \item Sample loading
 \item Normalisation
 \item Figure creation
-\item Differential expression analysis for the hcosen contrasts
+\item Differential expression analysis for the chosen contrasts
 }
 }
diff --git a/man/de_analysis.Rd b/man/de_analysis.Rd
index d9784938861da49dd545f4eeb87afb14c54809d0..fb7e89a78201adb68cd6bb3c18a0031935add7f4 100644
--- a/man/de_analysis.Rd
+++ b/man/de_analysis.Rd
@@ -23,8 +23,17 @@ de_analysis(dds, my_contrast, output_folder, basemean_threshold, lfc_threshold)
 \item{basemean_threshold:}{The minimum basemean of gene to be knameept}
 }
 \value{
-A dataframe indicating The number of differentially expressed genes
-and the number of up and down regulated genes
+A list containing:
+\enumerate{
+\item at \code{data} key: A dataframe indicating The number of differentially
+expressed genes and the number of up and down regulated genes
+\item at \code{dds} key: The dds object corresponding to a DESeqDatase object
+obtained after running the DESeq function.
+\item at \code{results} key: A dataframe containing the results of DEseQ2 analysis
+but for all gene
+\item at \code{de_results} key: A dataframe containing only differentially expressed
+genes
+}
 }
 \description{
 Perform a DESeq2 analysis with a given contrast
diff --git a/man/de_analyzes.Rd b/man/de_analyzes.Rd
index 8cd416298cc7b18b78709c2aed39e8d79a67f35c..1facc3fdad8b9a08f7b13589ba10bba5201c6b72 100644
--- a/man/de_analyzes.Rd
+++ b/man/de_analyzes.Rd
@@ -13,14 +13,31 @@ de_analyzes(
 )
 }
 \arguments{
+\item{dds}{The dds object corresponding to a DESeqDatase object obtained
+after running the DESeq function.}
+
+\item{my_contrasts}{A list containing contrast vectors}
+
 \item{output_folder}{Folder where the result table will be created}
 
 \item{lfc_threshold}{The minimum fold change to consider a gene significant}
 
-\item{my_contrast}{A list containing contrast vectors}
-
 \item{basemean_threshold:}{The minimum basemean of genes to be kept}
 }
+\value{
+A list containing for each comparison given in my_contrasts
+(keys of the list) a sublist containing:
+\enumerate{
+\item at \code{data} key: A dataframe indicating The number of differentially
+expressed genes and the number of up and down regulated genes
+\item at \code{dds} key: The dds object corresponding to a DESeqDataSet object
+obtained after running the DESeq function.
+\item at \code{results} key: A dataframe containing the results of DEseQ2 analysis
+but for all gene
+\item at \code{de_results} key: A dataframe containing only differentially expressed
+genes
+}
+}
 \description{
 Perform multiple differential expression analysis
 }
diff --git a/man/filter_dds.Rd b/man/filter_dds.Rd
index a3fffce5314ce1b32051270da125750752377881..807c75681a1853a53f3008437ac10f8baafdcb97 100644
--- a/man/filter_dds.Rd
+++ b/man/filter_dds.Rd
@@ -4,19 +4,20 @@
 \alias{filter_dds}
 \title{Filter DESeq2 object on expressed gene if needed}
 \usage{
-filter_dds(dds, filter_file, min_expression, addition_col, formula)
+filter_dds(dds, filter_list, min_expression, addition_col, my_formula)
 }
 \arguments{
 \item{dds}{A dds object}
 
-\item{filter_file}{A file containing genes}
+\item{filter_list}{A vector containing the list of genes to keep in the
+analysis. To keep all gene use a NULL object}
 
 \item{min_expression}{The minimum average required expression across all
 samples to keep the gene}
 
 \item{addition_col}{Additional design columns}
 
-\item{formula}{The formula to use in DESeq2}
+\item{my_formula}{The formula to use in DESeq2}
 }
 \value{
 A DESeqDataset object filtered
diff --git a/man/hline.Rd b/man/hline.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..cecc98c154de40cf35c36fbb725f284d56cd2d15
--- /dev/null
+++ b/man/hline.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/differiential_expression.R
+\name{hline}
+\alias{hline}
+\title{Function to draw a plotly horizontal line}
+\usage{
+hline(y = 0, color = "black")
+}
+\arguments{
+\item{y}{Location of horizontal line}
+
+\item{color}{Color of horizontal line}
+}
+\value{
+a list containing plotly parameters
+}
+\description{
+Function to draw a plotly horizontal line
+}
diff --git a/man/load_matrix.Rd b/man/load_matrix.Rd
index 976867a7a8bfe6c954faa57365a024d6d96dea31..59a93f6b9c1e3f7e5374ee4d1936dcdc1d0ae336 100644
--- a/man/load_matrix.Rd
+++ b/man/load_matrix.Rd
@@ -4,14 +4,15 @@
 \alias{load_matrix}
 \title{Build the deseq2 count matrix from design file}
 \usage{
-load_matrix(design, path, formula)
+load_matrix(design_table, path, my_formula)
 }
 \arguments{
-\item{design}{A design file with the column count_files, sample and condition}
+\item{design_table}{A dataframe with the column count_files, sample and
+condition. Other columns corresponding to cofactors can be present}
 
 \item{path}{The path were the count file are stored}
 
-\item{formula}{The formula to use in DESeq2}
+\item{my_formula}{The formula to use in DESeq2}
 }
 \value{
 A DESeqDataset object filtered
diff --git a/man/make_html_pca.Rd b/man/make_html_pca.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..44eac28f85e0e2b1d1341fd2566f652eda9e6c42
--- /dev/null
+++ b/man/make_html_pca.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plots.R
+\name{make_html_pca}
+\alias{make_html_pca}
+\title{Create plotly PCA plot}
+\usage{
+make_html_pca(pca_data, percent_var, output_folder, columns)
+}
+\arguments{
+\item{pca_data}{Object returned by DESeq2::plotPCA containing PCA table}
+
+\item{percent_var}{Vector containing the percentage of variance
+of PC1 and PC2}
+
+\item{output_folder}{Folder where the figure will be created}
+
+\item{columns}{The design columns}
+}
+\description{
+Create plotly PCA plot
+}
diff --git a/man/make_pca.Rd b/man/make_pca.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..f312f9f4c903ed41de09c895b9b9f0976119b9cc
--- /dev/null
+++ b/man/make_pca.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plots.R
+\name{make_pca}
+\alias{make_pca}
+\title{Make ggplot PCA}
+\usage{
+make_pca(pca_data, percent_var, columns, dds)
+}
+\arguments{
+\item{pca_data}{Object returned by DESeq2::plotPCA containing PCA table}
+
+\item{percent_var}{Vector containing the percentage of variance
+of PC1 and PC2}
+
+\item{columns}{A vector containing the columns to display in PCA data}
+
+\item{dds}{a DESeqDataSet object}
+}
+\description{
+Make ggplot PCA
+}
diff --git a/man/run_deseq2.Rd b/man/run_deseq2.Rd
index e9b18c1da2a840ed08c2bc789b0c79334932b980..e139a16338b94b3f4b75ad558c5af4950eb97ff9 100644
--- a/man/run_deseq2.Rd
+++ b/man/run_deseq2.Rd
@@ -5,36 +5,55 @@
 \title{DESeq2 wrapper}
 \usage{
 run_deseq2(
-  design,
+  design_table,
   path,
-  formula,
-  filter_file,
-  min_expression,
-  output_folder,
   my_contrasts,
-  basemean_threshold,
-  lfc_threshold
+  my_formula = "~ condition",
+  filter_list = NULL,
+  min_expression = 2,
+  output_folder = ".",
+  basemean_threshold = 0,
+  lfc_threshold = 0
 )
 }
 \arguments{
-\item{design}{A design file with the column count_files, sample and condition}
+\item{design_table}{A dataframe with the column count_files, sample and
+condition. Other columns corresponding to cofactors can be present}
 
 \item{path}{The path were the count file are stored}
 
-\item{formula}{The formula to use in DESeq2}
+\item{my_formula}{The formula to use in DESeq2 (default '~ condition')}
 
-\item{filter_file}{A file containing genes}
+\item{filter_list}{A vector containing the list of genes to keep in the
+analysis. To keep all gene use a NULL object, (default NULL)}
 
 \item{min_expression}{The minimum average required expression across
-all samples to keep the gene}
+all samples to keep the gene (default 2)}
 
-\item{output_folder}{Folder were the matrices will be produced}
+\item{output_folder}{Folder were the matrices will be produced (default .)}
 
-\item{lfc_threshold}{The minimum fold change to consider a gene significant}
+\item{lfc_threshold}{The minimum fold change to consider a gene significant
+(default 0)}
 
-\item{my_contrast}{A list containing contrast vectors}
+\item{my_contrast}{A list containing contrast vectors: you can use
+list(c('condition', 'TEST', 'CTRL') to build it)}
 
-\item{basemean_threshold:}{The minimum basemean of genes to be kept}
+\item{basemean_threshold:}{The minimum basemean of genes to be kept
+(default 0)}
+}
+\value{
+A list containing for each comparison given in my_contrasts
+(keys of the list) a sublist containing:
+\enumerate{
+\item at \code{data} key: A dataframe indicating The number of differentially
+expressed genes and the number of up and down regulated genes
+\item at \code{dds} key: The dds object corresponding to a DESeqDatase object
+obtained after running the DESeq function.
+\item at \code{results} key: A dataframe containing the results of DEseQ2 analysis
+but for all gene
+\item at \code{de_results} key: A dataframe containing only differentially expressed
+genes
+}
 }
 \description{
 DESeq2 wrapper
@@ -45,6 +64,6 @@ perform a complete DESeq2 analysis including:
 \item Sample loading
 \item Normalisation
 \item Figure creation
-\item Differential expression analysis for the hcosen contrasts
+\item Differential expression analysis for the chosen contrasts
 }
 }
diff --git a/man/vline.Rd b/man/vline.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..bc6a8eabcf1ae4fee5ee9aa4a1d963f2104fc091
--- /dev/null
+++ b/man/vline.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/differiential_expression.R
+\name{vline}
+\alias{vline}
+\title{Function to draw a plotly horizontal line}
+\usage{
+vline(x = 0, color = "black")
+}
+\arguments{
+\item{x}{Location of vertical line}
+
+\item{color}{Color of vertical line}
+}
+\value{
+a list containing plotly parameters
+}
+\description{
+Function to draw a plotly horizontal line
+}