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Update gmt #6

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Merged
federicomarini merged 4 commits into from
Feb 10, 2026
Merged

Update gmt #6

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3317b2c
retrieving gmt file from a more up to date version of wikipathways
federicomarini Nov 27, 2025
20b9319
bumped version of roxygen
federicomarini Nov 27, 2025
5170c9f
bump also package version number for completeness
federicomarini Nov 27, 2025
197383a
swapping the labels of the axes for grouped_distributions()
federicomarini Nov 27, 2025
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: CIA
Title: Cluster Independent Annotation (CIA) to Accurately Classify Cells in
scRNA-seq Datasets Using Gene Signatures
Version: 0.3.0
Version: 0.3.1
Authors@R:
c(
person(
Expand Down Expand Up @@ -33,7 +33,7 @@ Description: CIA (Cluster Independent Annotation) is designed to accurately
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
RoxygenNote: 7.3.3
Imports:
SingleCellExperiment,
SummarizedExperiment,
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2 changes: 1 addition & 1 deletion R/CIA_core.R
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@
#' signatures
#'
#' gmt_url <-
#' "https://data.wikipathways.org/20240710/gmt/wikipathways-20240710-gmt-Homo_sapiens.gmt"
#' "https://data.wikipathways.org/20251110/gmt/wikipathways-20251110-gmt-Homo_sapiens.gmt"
#'
#' sig_wikipathways <- load_signatures(gmt_url)
#' head(names(sig_wikipathways))
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4 changes: 2 additions & 2 deletions R/CIA_metrics.R
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Expand Up @@ -584,8 +584,8 @@ grouped_distributions <- function(data,
theme_minimal() +
labs(
title = "Median score values",
x = "Signatures",
y = ref_obs
x = ref_obs,
y = "Signatures"
)

## Save or display plot
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2 changes: 1 addition & 1 deletion man/load_signatures.Rd
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