@@ -42,7 +42,7 @@
 			"category": "gn9FXwemlVazWQIo",
 			"name": "Clean up column names",
 			"param_name": "cleanup_column_names",
-			"description": "Automatically alter invalid column names by adding X prefix to names starting with numerals and replacing special characters (-,:. ) with underscores",
+			"description": "Invalid raw counts column names can cause errors in downstream analysis. If TRUE, invalid column names are automatically altered by adding X to names that begin with a numeral and replacing special characters (-,:. ) with underscores. Invalid sample names and changes made will be reported.",
 			"type": "list",
 			"value_type": "string",
 			"default_value": "TRUE",
@@ -56,7 +56,7 @@
 			"category": "gn9FXwemlVazWQIo",
 			"name": "Split gene names",
 			"param_name": "split_gene_name",
-			"description": "Split the gene name column by special characters: ,|_-:",
+			"description": "If TRUE, split the gene name column by any of these special characters: ,|_-:",
 			"type": "list",
 			"value_type": "string",
 			"default_value": "TRUE",
@@ -70,7 +70,7 @@
 			"category": "gn9FXwemlVazWQIo",
 			"name": "Aggregate duplicate gene names",
 			"param_name": "aggregate_rows_with_duplicate_gene_names",
-			"description": "Sum counts across duplicate Feature ID rows into a single row within each sample",
+			"description": "If a Feature ID is duplicated on multiple rows of the raw counts, the log will report these Feature IDs. When TRUE, counts for duplicate Feature IDs are aggregated into a single row by summing counts across duplicate rows within each sample. Additional identifier columns, if present, are preserved and multiple matching identifiers appear as comma-separated values.",
 			"help_text": "When TRUE, additional identifier columns (e.g. Ensembl IDs) are preserved and multiple matching identifiers appear as comma-separated values.",
 			"type": "list",
 			"value_type": "string",
@@ -85,8 +85,8 @@
 			"category": "gn9FXwemlVazWQIo",
 			"name": "Column for collapsing duplicates",
 			"param_name": "gene_name_column_to_use_for_collapsing_duplicates",
-			"description": "Column with Feature IDs to use as grouping elements to collapse the counts matrix",
-			"help_text": "Leave blank to use the Feature ID column by default. If the Feature ID column can be split, the non-Ensembl ID name will be used. If no Ensembl IDs are detected, split IDs will be named Feature_id_1 and Feature_id_2.",
+			"description": "Select the column with Feature IDs to use as grouping elements to collapse the counts matrix. The log output lists columns available to identify duplicate row IDs for aggregation.",
+			"help_text": "Leaving this empty uses the Feature ID column. If the Feature ID column can be split, the non-Ensembl ID name will be used. If no Ensembl IDs are detected, split IDs will be named Feature_id_1 and Feature_id_2.",
 			"type": "text",
 			"value_type": "string"
 		},
@@ -95,8 +95,8 @@
 			"category": "Visualization",
 			"name": "Group column name",
 			"param_name": "group_colname",
-			"description": "Column from sample metadata used to color the read-depth plot",
-			"help_text": "Leave blank to use one color for all samples.",
+			"description": "Sample metadata column used to color the read-depth plot.",
+			"help_text": "Leaving this empty uses one color for all samples.",
 			"type": "text",
 			"value_type": "string",
 			"default_value": "Group"
@@ -106,8 +106,8 @@
 			"category": "Visualization",
 			"name": "Colors for read-depth plot",
 			"param_name": "colors_for_plots",
-			"description": "Comma-separated list of colors for read-depth groups",
-			"help_text": "Use color names or hex codes. Leave blank to use defaults.",
+			"description": "Optional colors used when group_colname is supplied. Named vectors are matched to group values; unnamed vectors follow group order and are extended with MOSuite colors when too few colors are supplied.",
+			"help_text": "Use color names or hex codes. Leaving this empty uses stored MOSuite colors.",
 			"type": "text",
 			"value_type": "string",
 			"default_value": "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500"
@@ -117,7 +117,7 @@
 			"category": "XqgPq28Eo5VCFSZu",
 			"name": "count type",
 			"param_name": "count_type",
-			"description": "which counts to clean. Must be a count type in names(moo@counts)",
+			"description": "The type of counts to use. Must be a name in the counts slot, moo@counts.",
 			"type": "text",
 			"value_type": "string",
 			"default_value": "raw"
@@ -127,8 +127,8 @@
 			"category": "XqgPq28Eo5VCFSZu",
 			"name": "Sample ID Column Name",
 			"param_name": "sample_id_colname",
-			"description": "Column name in the sample metadata containing sample IDs",
-			"help_text": "Leave blank to use the first column in the sample metadata by default",
+			"description": "The column from the sample metadata containing the sample names. The names in this column must exactly match the names used as sample column names in the input counts matrix.",
+			"help_text": "Leaving this empty uses the first column in the sample metadata.",
 			"type": "text",
 			"value_type": "string"
 		},
@@ -137,8 +137,8 @@
 			"category": "XqgPq28Eo5VCFSZu",
 			"name": "Feature ID column name",
 			"param_name": "feature_id_colname",
-			"description": "Column name in the counts matrix containing feature IDs",
-			"help_text": "Leave blank to use the first column by default",
+			"description": "The column from the counts data containing the Feature IDs, usually Gene or Protein ID. This is usually the first column of the input counts matrix.",
+			"help_text": "Leaving this empty uses the first column in the counts matrix.",
 			"type": "text",
 			"value_type": "string"
 		},
@@ -147,7 +147,7 @@
 			"category": "XqgPq28Eo5VCFSZu",
 			"name": "Samples to rename",
 			"param_name": "samples_to_rename",
-			"description": "Sample names to rename (advanced)",
+			"description": "Use this parameter to rename samples manually. Provide mappings in the format old_name: new_name; add each additional sample renaming as another item or comma-separated mapping.",
 			"type": "text",
 			"value_type": "string"
 		}
 
@@ -2,6 +2,7 @@
 
 ## Development version
 
+- Sync Code Ocean app panel parameter descriptions with MOSuite package documentation for MOSuite v0.4.1 (#8, @phoman14).
 - Fixed the Code Ocean panel so parameters are passed to `main.R` by name instead of as positional values (#2, @phoman14).
 - Improved the Code Ocean parameter UI for the clean capsule (#2, @phoman14).
 - Added read-depth plot group color controls to the Visualization panel (#2, @phoman14).