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Update diff counts capsule parameter UI #3

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Update diff counts capsule parameter UI #3

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71854ab
Update count_type to list with raw, clean, filt options (default: filt)
phoman14 Jun 29, 2026
6076e02
Move count_type to first position in Basic category
phoman14 Jun 29, 2026
00cdcc0
Use list controls for differential parameters
phoman14 Jun 30, 2026
4740ab0
Order diff normalization options
phoman14 Jun 30, 2026
c4b87c2
Clarify diff normalization methods
phoman14 Jun 30, 2026
0a97378
Update changelog for parameter UI changes
phoman14 Jun 30, 2026
959b86c
Add author handle to changelog entry
phoman14 Jun 30, 2026
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65 changes: 44 additions & 21 deletions .codeocean/app-panel.json
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Original file line number Diff line number Diff line change
Expand Up @@ -16,21 +16,36 @@
"id": "7Rr6IxOMDucKMImp",
"name": "Input Data Parameters",
"description": "Options for defining input data",
"icon": "📁"
"icon": "\ud83d\udcc1"
},
{
"id": "EzTg1ivlFDHEy9PI",
"name": "Basic",
"icon": "📂"
"icon": "\ud83d\udcc2"
},
{
"id": "FvI4Z2eb9sjL47Jt",
"name": "Advanced",
"description": "Advanced parameters",
"icon": "📂"
"icon": "\ud83d\udcc2"
}
],
"parameters": [
{
"id": "qsXhqvyKgDh3Vz8u",
"category": "EzTg1ivlFDHEy9PI",
"name": "Count type",
"param_name": "count_type",
"description": "Counts slot name to use for differential expression (e.g., filt)",
"type": "list",
"value_type": "string",
"default_value": "filt",
"extra_data": [
"raw",
"clean",
"filt"
]
},
{
"id": "73xRrg0JvDvhEkPN",
"category": "EzTg1ivlFDHEy9PI",
Expand Down Expand Up @@ -65,16 +80,6 @@
"default_value": "Group,Batch",
"required": true
},
{
"id": "qsXhqvyKgDh3Vz8u",
"category": "FvI4Z2eb9sjL47Jt",
"name": "Count type",
"param_name": "count_type",
"description": "Counts slot name to use for differential expression (e.g., filt)",
"type": "text",
"value_type": "string",
"default_value": "filt"
},
{
"id": "WoZUI91NYysibcVj",
"category": "FvI4Z2eb9sjL47Jt",
Expand Down Expand Up @@ -117,34 +122,52 @@
"name": "Input in log counts",
"param_name": "input_in_log_counts",
"description": "Set TRUE if counts are already log2-transformed",
"type": "text",
"type": "list",
"value_type": "string",
"default_value": "FALSE"
"default_value": "FALSE",
"extra_data": [
"TRUE",
"FALSE"
]
},
{
"id": "yxhLfINFuSTTS3Fj",
"category": "FvI4Z2eb9sjL47Jt",
"name": "Return mean and sd",
"param_name": "return_mean_and_sd",
"description": "Return group means and standard deviations in addition to DE estimates",
"type": "text",
"type": "list",
"value_type": "string",
"default_value": "FALSE"
"default_value": "FALSE",
"extra_data": [
"TRUE",
"FALSE"
]
},
{
"id": "Uq2LuAF8ff8pzM9e",
"category": "FvI4Z2eb9sjL47Jt",
"name": "voom normalization method",
"param_name": "voom_normalization_method",
"description": "Normalization method passed to limma::voom",
"type": "text",
"description": "Normalization method for differential expression. edgeR methods are applied with calcNormFactors before voom; limma methods are passed to voom normalize. limma options: quantile, scale, cyclicloess, none. edgeR options: TMM, TMMwzp, RLE, upperquartile.",
"type": "list",
"value_type": "string",
"default_value": "quantile"
"default_value": "quantile",
"extra_data": [
"quantile",
"scale",
"cyclicloess",
"none",
"TMM",
"TMMwzp",
"RLE",
"upperquartile"
]
}
],
"results": [
{
"file_name": "figures/diff/mean-variance.png"
}
]
}
}
6 changes: 5 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,9 @@
# Code Ocean capsule - MOSuite - differential expression analysis

## Development version

- Improved the Code Ocean parameter UI for the diff counts capsule (#3, @phoman14).

## v3.0

- The MOSuite package is now available in `code/MOSuite`. (#2)
Expand All @@ -17,4 +21,4 @@
- Initial release.
- Uses MOSuite v0.2.1-dev docker image.

<https://poc-nci.codeocean.io/capsule/6218465/tree/v1> `8f9bdf7`
<https://poc-nci.codeocean.io/capsule/6218465/tree/v1> `8f9bdf7`
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