diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index c29d88f..d026c43 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -57,7 +57,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows' && matrix.config.image == null
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }}
diff --git a/NAMESPACE b/NAMESPACE
index 584b4a3..2b4a2ed 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -53,6 +53,7 @@ importFrom(clusterProfiler,enrichGO)
 importFrom(ggforce,geom_sina)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,coord_cartesian)
+importFrom(ggplot2,element_text)
 importFrom(ggplot2,geom_boxplot)
 importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_point)
@@ -64,6 +65,7 @@ importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,position_jitter)
+importFrom(ggplot2,rel)
 importFrom(ggplot2,scale_color_discrete)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_colour_manual)
@@ -72,6 +74,7 @@ importFrom(ggplot2,scale_x_discrete)
 importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,scale_y_log10)
 importFrom(ggplot2,stat_summary)
+importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_classic)
 importFrom(ggplot2,xlab)
diff --git a/R/color_mgmt.R b/R/color_mgmt.R
index 7cdbdaf..f273553 100644
--- a/R/color_mgmt.R
+++ b/R/color_mgmt.R
@@ -189,19 +189,39 @@ de_table_painter <- function(res_de,
                              ) {
   ## Checks on the input parameters
 
-  res_de <- res_de[order(res_de$padj), ]
-  my_dt <- DT::datatable(
-    as.data.frame(res_de),
-    escape = FALSE,
-    options = list(
-      scrollX = TRUE,
-      scrollY = "400px",
-      pageLength = 25,
-      columnDefs = list(
-        list(className = "dt-center", targets = "_all")
+  if (is(res_de, "DESeqResults")) {
+    res_de <- res_de[order(res_de$padj), ]
+    my_dt <- DT::datatable(
+      as.data.frame(res_de),
+      escape = FALSE,
+      options = list(
+        scrollX = TRUE,
+        scrollY = "400px",
+        pageLength = 25,
+        columnDefs = list(
+          list(className = "dt-center", targets = "_all")
+        )
       )
     )
-  )
+  } else if ((is(res_de, "DGELRT")) | (is(res_de, "DGEEXACT"))) {
+    # TODO: any conversion
+    # TODO: possibly also re-change the default values of the column names where to find things in
+    message("Working with edgeR objects, remove me later")
+  } else {
+    res_de <- res_de[order(res_de$padj), ]
+    my_dt <- DT::datatable(
+      as.data.frame(res_de),
+      escape = FALSE,
+      options = list(
+        scrollX = TRUE,
+        scrollY = "400px",
+        pageLength = 25,
+        columnDefs = list(
+          list(className = "dt-center", targets = "_all")
+        )
+      )
+    )
+  }
 
   if (!is.null(rounding_digits)) {
     my_dt <- formatRound(
diff --git a/R/de2df.R b/R/de2df.R
index 0c1d338..04b7a57 100644
--- a/R/de2df.R
+++ b/R/de2df.R
@@ -39,3 +39,14 @@ deresult_to_df <- function(res_de, FDR = NULL) {
   }
   res
 }
+
+.deresult_to_df.DESeq <- function() {
+
+}
+
+.deresult_to_df.edgeR <- function() {
+
+}
+
+
+
diff --git a/R/expression_summaries.R b/R/expression_summaries.R
index d8573e1..6d7ebcc 100644
--- a/R/expression_summaries.R
+++ b/R/expression_summaries.R
@@ -71,6 +71,3 @@ pair_corr <- function(df, log = TRUE, method = "pearson", use_subset = TRUE) {
         xlim = c(rangeMin, rangeMax),
         ylim = c(rangeMin, rangeMax))
 }
-
-
-## couple more TODO
diff --git a/R/gene_annotation.R b/R/gene_annotation.R
index 019b99d..e76aad6 100644
--- a/R/gene_annotation.R
+++ b/R/gene_annotation.R
@@ -38,6 +38,15 @@ get_annotation_orgdb <- function(de_container,
                                  orgdb_package,
                                  id_type,
                                  key_for_genenames = "SYMBOL") {
+
+  ## TODO: see if we need any checks
+  if (is(de_container, "DESeqDataSet")) {
+    ## TODO
+    # all we need is rownames
+  }
+
+
+
   if (is.null(orgdb_package))
     stop("Select an annotation package to generate the corresponding annotation")
 
diff --git a/R/gene_plot.R b/R/gene_plot.R
index 1144291..e5f1778 100644
--- a/R/gene_plot.R
+++ b/R/gene_plot.R
@@ -35,6 +35,7 @@
 #' @param return_data Logical, whether the function should just return the
 #' data.frame of expression values and covariates for custom plotting. Defaults
 #' to FALSE.
+#' @param color_by TODO - if we keep this in for the final version?
 #'
 #' @return A `ggplot` object
 #' @export
@@ -42,7 +43,7 @@
 #' @importFrom stats median
 #' @importFrom ggplot2 ggplot aes geom_point geom_boxplot geom_violin
 #' geom_text position_jitter scale_color_discrete scale_x_discrete scale_y_log10
-#' scale_y_continuous stat_summary theme_bw labs
+#' scale_y_continuous stat_summary theme theme_bw labs element_text rel
 #' @importFrom ggrepel geom_text_repel
 #' @importFrom ggforce geom_sina
 #' @importFrom rlang .data
@@ -80,41 +81,78 @@
 #'   annotation_obj = anno_df
 #' )
 gene_plot <- function(de_container,
-                      gene,
-                      intgroup = NULL,
-                      assay = "counts",
-                      annotation_obj = NULL,
-                      normalized = TRUE,
-                      transform = TRUE,
-                      labels_display = TRUE,
-                      labels_repel = TRUE,
-                      plot_type = "auto",
-                      return_data = FALSE) {
-  if (!is(de_container, "DESeqDataSet")) {
-    stop("The provided `de_container` is not a DESeqDataSet object, please check your input parameters.")
+                                gene,
+                                intgroup = NULL,
+                                assay = "counts",
+                                annotation_obj = NULL,
+                                normalized = TRUE,
+                                transform = TRUE,
+                                labels_display = TRUE,
+                                labels_repel = TRUE,
+                                plot_type = "auto",
+                                return_data = FALSE,
+                                color_by = NULL) {
+  if (!is(de_container, "DESeqDataSet") && !is(de_container, "EList") && !is(de_container, "DGEList")) {
+    stop("The provided `de_container` must be a DESeqDataSet, EList, or DGEList object. Please check your input parameters.")
   }
 
   if (is.null(intgroup)) {
-    # gently fall back to the first colData element if it is there
-    if (length(names(colData(de_container))) > 0) {
-      intgroup <- names(colData(de_container))[1]
-      message("Defaulting to '", intgroup, "' as the `intgroup` parameter...")
-    } else {
-      stop("No colData has been provided, therefore `intgroup` cannot be selected properly")
+    if (is(de_container, "DESeqDataSet")) {
+      if (length(names(colData(de_container))) > 0) {
+        intgroup <- names(colData(de_container))[1]
+        message("Defaulting to '", intgroup, "' as the `intgroup` parameter...")
+      } else {
+        stop("No colData has been provided, therefore `intgroup` cannot be selected properly.")
+      }
+    } else if (is(de_container, "EList") || is(de_container, "DGEList")) {
+      if (length(names(de_container$samples)) > 0) {
+        intgroup <- names(de_container$samples)[1]
+        message("Defaulting to '", intgroup, "' as the `intgroup` parameter...")
+      } else {
+        stop("No sample information has been provided, therefore `intgroup` cannot be selected properly.")
+      }
     }
   }
 
+  if (is.null(color_by)) {
+    color_by <- intgroup
+  }
+
   plot_type <- match.arg(
     plot_type,
     c("auto", "jitteronly", "boxplot", "violin", "sina")
   )
 
-  if (!(all(intgroup %in% colnames(colData(de_container))))) {
-    stop(
-      "`intgroup` not found in the colData slot of the de_container object",
-      "\nPlease specify one of the following: \n",
-      paste0(colnames(colData(de_container)), collapse = ", ")
-    )
+  if (is(de_container, "DESeqDataSet")) {
+    if (!(all(intgroup %in% colnames(colData(de_container))))) {
+      stop(
+        "`intgroup` not found in the colData slot of the de_container object",
+        "\nPlease specify one of the following: \n",
+        paste0(colnames(colData(de_container)), collapse = ", ")
+      )
+    }
+    if (!(color_by %in% colnames(colData(de_container)))) {
+      stop(
+        "`color_by` not found in the colData slot of the de_container object",
+        "\nPlease specify one of the following: \n",
+        paste0(colnames(colData(de_container)), collapse = ", ")
+      )
+    }
+  } else if (is(de_container, "EList") || is(de_container, "DGEList")) {
+    if (!(all(intgroup %in% colnames(de_container$samples)))) {
+      stop(
+        "`intgroup` not found in the samples slot of the de_container object",
+        "\nPlease specify one of the following: \n",
+        paste0(colnames(de_container$samples), collapse = ", ")
+      )
+    }
+    if (!(color_by %in% colnames(de_container$samples))) {
+      stop(
+        "`color_by` not found in the samples slot of the de_container object",
+        "\nPlease specify one of the following: \n",
+        paste0(colnames(de_container$samples), collapse = ", ")
+      )
+    }
   }
 
   df <- get_expr_values(
@@ -136,28 +174,23 @@ gene_plot <- function(de_container,
   df$plotby <- interaction(onlyfactors)
 
   min_by_groups <- min(table(df$plotby))
-  # depending on this, use boxplots/nothing/violins/sina
 
   if (return_data) {
     return(df)
   }
 
-  p <- ggplot(df, aes(x = .data$plotby, y = .data$exp_value, col = .data$plotby)) +
+  p <- ggplot(df, aes(x = .data$plotby, y = .data$exp_value, col = .data[[color_by]])) +
     scale_x_discrete(name = "") +
     scale_color_discrete(name = "Experimental\ngroup") +
     theme_bw()
 
-  # for connected handling of jittered points AND labels
   jit_pos <- position_jitter(width = 0.2, height = 0, seed = 42)
 
-  # somewhat following the recommendations here
-  # https://www.embopress.org/doi/full/10.15252/embj.201694659
   if (plot_type == "jitteronly" || (plot_type == "auto" & min_by_groups <= 3)) {
     p <- p +
       geom_point(aes(x = .data$plotby, y = .data$exp_value),
-        position = jit_pos
+                 position = jit_pos
       )
-    # do nothing - or add a line for the median?
   } else if (plot_type == "boxplot" || (plot_type == "auto" & (min_by_groups > 3 & min_by_groups < 10))) {
     p <- p +
       geom_boxplot(outlier.shape = NA) +
@@ -179,17 +212,16 @@ gene_plot <- function(de_container,
       )
   }
 
-  # handling the labels
   if (labels_display) {
     if (labels_repel) {
       p <- p + ggrepel::geom_text_repel(aes(label = .data$sample_id),
-        min.segment.length = 0,
-        position = jit_pos
+                                        min.segment.length = 0,
+                                        position = jit_pos
       )
     } else {
       p <- p + geom_text(aes(label = .data$sample_id),
-        hjust = -0.1, vjust = 0.1,
-        position = jit_pos
+                         hjust = -0.1, vjust = 0.1,
+                         position = jit_pos
       )
     }
   }
@@ -204,24 +236,38 @@ gene_plot <- function(de_container,
     assay
   }
 
-  # handling y axis transformation
   if (transform) {
     p <- p + scale_y_log10(name = paste0(y_label, " (log10 scale)"))
   } else {
     p <- p + scale_y_continuous(name = y_label)
   }
 
-  # handling the displayed names and ids
   if (!is.null(annotation_obj)) {
     p <- p + labs(title = paste0(genesymbol, " - ", gene))
   } else {
     p <- p + labs(title = paste0(gene))
   }
 
+  p <- p + stat_summary(
+    fun = mean, geom = "line", aes(group = 1),
+    color = "grey80", linewidth = 0.8
+  ) +
+    theme_bw() +
+    theme(
+      axis.title.x = element_text(size = rel(1.6)),
+      axis.title.y = element_text(size = rel(1.6)),
+      axis.text.x = element_text(size = rel(1.6)),
+      axis.text.y = element_text(size = rel(1.6)),
+      strip.text.x = element_text(size = rel(1.6)),
+      strip.text.y = element_text(size = rel(1.6)),
+      legend.text = element_text(size = rel(1.4)),
+      legend.title = element_text(size = rel(1.4)),
+      plot.title = element_text(size = rel(1.6))
+    )
+
   return(p)
 }
 
-
 #' Get expression values
 #'
 #' Extract expression values, with the possibility to select other assay slots
@@ -245,9 +291,6 @@ gene_plot <- function(de_container,
 #'
 #' @export
 #'
-#' @importFrom DESeq2 counts estimateSizeFactors sizeFactors normalizationFactors
-#' @importFrom SummarizedExperiment colData assays
-#'
 #' @examples
 #' library("macrophage")
 #' library("DESeq2")
@@ -273,6 +316,43 @@ get_expr_values <- function(de_container,
                             intgroup,
                             assay = "counts",
                             normalized = TRUE) {
+
+  # TODO: generic checks could go here:
+  # e.g. on gene, intgroup, assay (they have to be strings)
+
+  #
+  if (is(de_container, "DESeqDataSet")) {
+    exp_df <- .get_expr_values.DESeqDataSet(de_container = de_container,
+                                            gene = gene,
+                                            intgroup = intgroup,
+                                            assay = assay,
+                                            normalized = normalized)
+  } else if (is(de_container, "DGEList")) {
+    # TODO
+    ## add the behavior here (can be as schematic as the call above, the real
+    ## behavior is defined in the function itself - below)
+    exp_df <- .get_expr_values.DGEList()
+  } else {
+    # TODO
+    ## return an error to say the object has to be one of the supported types
+    stop("The object provided ... TODO")
+  }
+
+  return(exp_df)
+}
+
+
+#' get_expr_values, from a DESeqDataSet object
+#'
+#' @importFrom DESeq2 counts estimateSizeFactors sizeFactors normalizationFactors
+#' @importFrom SummarizedExperiment colData assays
+#'
+#' @keywords internal
+.get_expr_values.DESeqDataSet <- function(de_container,
+                                          gene,
+                                          intgroup,
+                                          assay,
+                                          normalized) {
   if (!(assay %in% names(assays(de_container)))) {
     stop(
       "Please specify a name of one of the existing assays: \n",
@@ -298,3 +378,57 @@ get_expr_values <- function(de_container,
 
   return(exp_df)
 }
+
+#' get_expr_values, from an Elist object
+#'
+#' @importFrom DESeq2 counts estimateSizeFactors sizeFactors normalizationFactors
+#' @importFrom SummarizedExperiment colData assays
+#'
+#' @keywords internal
+.get_expr_values.EList <- function(## define the parameters "cleverly"
+                                  ) {
+  # TODO
+  ## add the behavior here
+}
+
+#' get_expr_values, from a DGEList object
+#'
+#' @importFrom DESeq2 counts estimateSizeFactors sizeFactors normalizationFactors
+#' @importFrom SummarizedExperiment colData assays
+#'
+#' @keywords internal
+.get_expr_values.DGEList <- function(## define the parameters "cleverly"
+                                    ) {
+  # TODO
+  ## add the behavior here
+}
+
+
+## This is the ongoing implementation:
+
+### # Function to get expression values based on the container type
+###   get_expr_values <- function(de_container, gene, intgroup, assay, normalized) {
+###     if (is(de_container, "DESeqDataSet")) {
+###       if (assay == "counts") {
+###         values <- counts(de_container, normalized = normalized)
+###       } else {
+###         values <- assay(de_container, assay)
+###       }
+###       intgroup_values <- colData(de_container)[, intgroup, drop = FALSE]
+###       color_by_values <- colData(de_container)[, color_by, drop = FALSE]
+###     } else if (is(de_container, "EList")) {
+###       values <- de_container$E[gene, , drop = FALSE]
+###       intgroup_values <- de_container$samples[, intgroup, drop = FALSE]
+###       color_by_values <- de_container$samples[, color_by, drop = FALSE]
+###     } else if (is(de_container, "DGEList")) {
+###       values <- de_container$counts[gene, , drop = FALSE]
+###       if (normalized) {
+###         values <- cpm(de_container, normalized.lib.sizes = TRUE)[gene, , drop = FALSE]
+###       }
+###       intgroup_values <- de_container$samples[, intgroup, drop = FALSE]
+###       color_by_values <- de_container$samples[, color_by, drop = FALSE]
+###     }
+###     df <- data.frame(exp_value = as.numeric(values), intgroup_values, color_by_values)
+###     rownames(df) <- colnames(values)
+###     return(df)
+###   }
diff --git a/man/dot-get_expr_values.DESeqDataSet.Rd b/man/dot-get_expr_values.DESeqDataSet.Rd
new file mode 100644
index 0000000..c10edb1
--- /dev/null
+++ b/man/dot-get_expr_values.DESeqDataSet.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gene_plot.R
+\name{.get_expr_values.DESeqDataSet}
+\alias{.get_expr_values.DESeqDataSet}
+\title{get_expr_values, from a DESeqDataSet object}
+\usage{
+.get_expr_values.DESeqDataSet(de_container, gene, intgroup, assay, normalized)
+}
+\description{
+get_expr_values, from a DESeqDataSet object
+}
+\keyword{internal}
diff --git a/man/dot-get_expr_values.DGEList.Rd b/man/dot-get_expr_values.DGEList.Rd
new file mode 100644
index 0000000..ed3723f
--- /dev/null
+++ b/man/dot-get_expr_values.DGEList.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gene_plot.R
+\name{.get_expr_values.DGEList}
+\alias{.get_expr_values.DGEList}
+\title{get_expr_values, from a DGEList object}
+\usage{
+.get_expr_values.DGEList()
+}
+\description{
+get_expr_values, from a DGEList object
+}
+\keyword{internal}
diff --git a/man/dot-get_expr_values.EList.Rd b/man/dot-get_expr_values.EList.Rd
new file mode 100644
index 0000000..403bf7f
--- /dev/null
+++ b/man/dot-get_expr_values.EList.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/gene_plot.R
+\name{.get_expr_values.EList}
+\alias{.get_expr_values.EList}
+\title{get_expr_values, from an Elist object}
+\usage{
+.get_expr_values.EList()
+}
+\description{
+get_expr_values, from an Elist object
+}
+\keyword{internal}
diff --git a/man/gene_plot.Rd b/man/gene_plot.Rd
index 82130e8..f1ab6dc 100644
--- a/man/gene_plot.Rd
+++ b/man/gene_plot.Rd
@@ -15,7 +15,8 @@ gene_plot(
   labels_display = TRUE,
   labels_repel = TRUE,
   plot_type = "auto",
-  return_data = FALSE
+  return_data = FALSE,
+  color_by = NULL
 )
 }
 \arguments{
@@ -58,6 +59,8 @@ samples in the smallest group defined via \code{intgroup}}
 \item{return_data}{Logical, whether the function should just return the
 data.frame of expression values and covariates for custom plotting. Defaults
 to FALSE.}
+
+\item{color_by}{TODO - if we keep this in for the final version?}
 }
 \value{
 A \code{ggplot} object