diff --git a/DESCRIPTION b/DESCRIPTION
index 1fa4b8d..772045e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: escape
 Title: Easy single cell analysis platform for enrichment
-Version: 2.5.3
+Version: 2.5.4
 Authors@R: c(
     person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"),
     person(given = "Jared", family = "Andrews", role = c("aut"), email = "jared.andrews07@gmail.com"),
diff --git a/NEWS.md b/NEWS.md
index 17b327a..98e3fae 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# 2.5.4  (2025-06-05)
+
+## Bug fixes
+* Fix conversion wide-to-long format for ```heatmapEnrichment()```
+* Fix issue with t() call on sparse matrices. 
+
 # 2.5.3  (2025-05-19)
 
 ## Highlights
diff --git a/R/heatmapEnrichment.R b/R/heatmapEnrichment.R
index be80a04..821f982 100644
--- a/R/heatmapEnrichment.R
+++ b/R/heatmapEnrichment.R
@@ -96,7 +96,7 @@ heatmapEnrichment <- function(input.data,
   # ---------- 4. long format for ggplot (base-R) --------------------------
   long <- data.frame(
     variable = rep(gene.set, each = nrow(agg)),
-    value    = as.vector(t(agg[gene.set])),
+    value    = unlist(agg[gene.set], use.names = FALSE),
     group    = rep(agg[[group.by]], times = length(gene.set)),
     stringsAsFactors = FALSE
   )
diff --git a/R/utils.R b/R/utils.R
index 483674c..c713793 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -185,7 +185,7 @@
     }
     loadNamespace("DelayedMatrixStats")
   }
-  cnts[MatrixGenerics::rowSums2(cnts) != 0, , drop = FALSE]
+  cnts[MatrixGenerics::rowSums2(cnts, na.rm = TRUE) != 0, , drop = FALSE]
 }
 
 # -----------------------------------------------------------------------------