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Feature/omics layers #45

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Merged
DanielGarbozo merged 3 commits into from
May 11, 2026
Merged

Feature/omics layers #45

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9bff5b1
add; nice_GenomeTrack.R, document, and tests
DanielGarbozo May 11, 2026
1059335
Merge remote-tracking branch 'upstream/dev' into feature/omics-layers
DanielGarbozo May 11, 2026
a56ab4b
fix: Mock biomaRt in get_annotations tests
DanielGarbozo May 11, 2026
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14 changes: 10 additions & 4 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,6 @@ Authors@R: c(
Description: This package contains functions that help in manipulating tables and generating plots for multi-omics analysis including genomics, transcriptomics, proteomics, methylomics and immunoinformatics.
License: CC BY-NC-SA 4.0
Encoding: UTF-8
RoxygenNote: 7.3.3
Imports:
dplyr,
ggplot2,
Expand All @@ -25,13 +24,18 @@ Imports:
graphics,
magrittr,
rlang,
stats,
umap,
tibble,
scales,
grid,
utils,
patchwork
patchwork,
Gviz,
rtracklayer,
GenomeInfoDb,
GenomicRanges,
stats,
S4Vectors
Suggests:
biomaRt,
circlize,
Expand All @@ -57,7 +61,8 @@ Suggests:
tidyselect,
tm,
testthat (>= 3.0.0),
withr
withr,
Rsamtools
Roxygen: list(markdown = TRUE)
Depends:
R (>= 4.4.0)
Expand All @@ -66,3 +71,4 @@ LazyDataCompression: xz
VignetteBuilder: knitr
URL: https://bigmindlab.github.io/OmicsKit
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
4 changes: 4 additions & 0 deletions NAMESPACE
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Expand Up @@ -19,6 +19,7 @@ export(merge_PA)
export(multiplot_PA)
export(network_clust)
export(network_clust_gg)
export(nice_GenomeTrack)
export(nice_KM)
export(nice_PCA)
export(nice_UMAP)
Expand All @@ -32,7 +33,10 @@ export(split_cases)
export(splot_PA)
export(tpm)
import(ggplot2)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,mcols)
importFrom(magrittr,"%>%")
importFrom(patchwork,plot_layout)
importFrom(rlang,.data)
importFrom(stats,na.omit)
importFrom(utils,modifyList)
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