multiDEGGs
Multi-Omic Differentially Expressed Gene-Gene Pairs
v1.2.0
·
Mar 24, 2026
·
GPL-3
Description
Performs multi-omic differential network analysis by revealing differential interactions between molecular entities (genes, proteins, transcription factors, or other biomolecules) across the omic datasets provided. For each omic dataset, a differential network is constructed where links represent statistically significant differential interactions between entities. These networks are then integrated into a comprehensive visualization using distinct colors to distinguish interactions from different omic layers. This unified display allows interactive exploration of cross-omic patterns, such as differential interactions present at both transcript and protein levels. For each link, users can access differential statistical significance metrics (p values or adjusted p values, calculated via robust or traditional linear regression with interaction term) and differential regression plots. The methods implemented in this package are described in Sciacca et al. (2023) <doi:10.1093/bioinformatics/btad192>.
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Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | ERROR |
| r-devel-linux-x86_64-debian-gcc | ERROR |
| r-devel-linux-x86_64-fedora-clang | ERROR |
| r-devel-linux-x86_64-fedora-gcc | ERROR |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | ERROR |
| r-release-linux-x86_64 | ERROR |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (18 non-OK)
NOTE
r-devel-linux-x86_64-debian-clang
Rd cross-references
Unknown package ‘nestedcv’ in Rd xrefs
ERROR
r-devel-linux-x86_64-debian-clang
examples
Running examples in ‘multiDEGGs-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiDEGGs_combined_filter
> ### Title: Combined multiDEGGs filter
> ### Aliases: multiDEGGs_combined_filter
>
> ### ** Examples
>
> library(nestedcv)
Error in library(nestedcv) : there is no package called ‘nestedcv’
Execution halted
ERROR
r-devel-linux-x86_64-debian-clang
re-building of vignette outputs
Error(s) in re-building vignettes:
...
--- re-building ‘Differential_Network_Analysis.Rmd’ using rmarkdown
--- finished re-building ‘Differential_Network_Analysis.Rmd’
--- re-building ‘Feature_Selection.Rmd’ using rmarkdown
Quitting from Feature_Selection.Rmd:95-117 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'nestedcv'
---
Backtrace:
▆
1. └─base::library(nestedcv)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Feature_Selection.Rmd' failed with diagnostics:
there is no package called 'nestedcv'
--- failed re-building ‘Feature_Selection.Rmd’
SUMMARY: processing the following file failed:
‘Feature_Selection.Rmd’
Error: Vignette re-building failed.
Execution halted
NOTE
r-devel-linux-x86_64-debian-gcc
Rd cross-references
Unknown package ‘nestedcv’ in Rd xrefs
ERROR
r-devel-linux-x86_64-debian-gcc
examples
Running examples in ‘multiDEGGs-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiDEGGs_combined_filter
> ### Title: Combined multiDEGGs filter
> ### Aliases: multiDEGGs_combined_filter
>
> ### ** Examples
>
> library(nestedcv)
Error in library(nestedcv) : there is no package called ‘nestedcv’
Execution halted
ERROR
r-devel-linux-x86_64-debian-gcc
re-building of vignette outputs
Error(s) in re-building vignettes:
...
--- re-building ‘Differential_Network_Analysis.Rmd’ using rmarkdown
--- finished re-building ‘Differential_Network_Analysis.Rmd’
--- re-building ‘Feature_Selection.Rmd’ using rmarkdown
Quitting from Feature_Selection.Rmd:95-117 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'nestedcv'
---
Backtrace:
▆
1. └─base::library(nestedcv)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Feature_Selection.Rmd' failed with diagnostics:
there is no package called 'nestedcv'
--- failed re-building ‘Feature_Selection.Rmd’
SUMMARY: processing the following file failed:
‘Feature_Selection.Rmd’
Error: Vignette re-building failed.
Execution halted
NOTE
r-devel-linux-x86_64-fedora-clang
Rd cross-references
Unknown package ‘nestedcv’ in Rd xrefs
ERROR
r-devel-linux-x86_64-fedora-clang
examples
Running examples in ‘multiDEGGs-Ex.R’ failed The error most likely occurred in: > ### Name: multiDEGGs_combined_filter > ### Title: Combined multiDEGGs filter > ### Aliases: multiDEGGs_combined_filter > > ### ** Examples > > library(nestedcv) Error in library(nestedcv) : there is no package called ‘nestedcv’ Execution halted
ERROR
r-devel-linux-x86_64-fedora-clang
re-building of vignette outputs
Error(s) in re-building vignettes:
--- re-building ‘Differential_Network_Analysis.Rmd’ using rmarkdown
--- finished re-building ‘Differential_Network_Analysis.Rmd’
--- re-building ‘Feature_Selection.Rmd’ using rmarkdown
Quitting from Feature_Selection.Rmd:95-117 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'nestedcv'
---
Backtrace:
▆
1. └─base::library(nestedcv)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Feature_Selection.Rmd' failed with diagnostics:
there is no package called 'nestedcv'
--- failed re-building ‘Feature_Selection.Rmd’
SUMMARY: processing the following file failed:
‘Feature_Selection.Rmd’
Error: Vignette re-building failed.
Execution halted
NOTE
r-devel-linux-x86_64-fedora-gcc
Rd cross-references
Unknown package ‘nestedcv’ in Rd xrefs
ERROR
r-devel-linux-x86_64-fedora-gcc
examples
Running examples in ‘multiDEGGs-Ex.R’ failed The error most likely occurred in: > ### Name: multiDEGGs_combined_filter > ### Title: Combined multiDEGGs filter > ### Aliases: multiDEGGs_combined_filter > > ### ** Examples > > library(nestedcv) Error in library(nestedcv) : there is no package called ‘nestedcv’ Execution halted
ERROR
r-devel-linux-x86_64-fedora-gcc
re-building of vignette outputs
Error(s) in re-building vignettes:
--- re-building ‘Differential_Network_Analysis.Rmd’ using rmarkdown
--- finished re-building ‘Differential_Network_Analysis.Rmd’
--- re-building ‘Feature_Selection.Rmd’ using rmarkdown
Quitting from Feature_Selection.Rmd:95-117 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'nestedcv'
---
Backtrace:
▆
1. └─base::library(nestedcv)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Feature_Selection.Rmd' failed with diagnostics:
there is no package called 'nestedcv'
--- failed re-building ‘Feature_Selection.Rmd’
SUMMARY: processing the following file failed:
‘Feature_Selection.Rmd’
Error: Vignette re-building failed.
Execution halted
NOTE
r-patched-linux-x86_64
Rd cross-references
Unknown package ‘nestedcv’ in Rd xrefs
ERROR
r-patched-linux-x86_64
examples
Running examples in ‘multiDEGGs-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiDEGGs_combined_filter
> ### Title: Combined multiDEGGs filter
> ### Aliases: multiDEGGs_combined_filter
>
> ### ** Examples
>
> library(nestedcv)
Error in library(nestedcv) : there is no package called ‘nestedcv’
Execution halted
ERROR
r-patched-linux-x86_64
re-building of vignette outputs
Error(s) in re-building vignettes:
...
--- re-building ‘Differential_Network_Analysis.Rmd’ using rmarkdown
--- finished re-building ‘Differential_Network_Analysis.Rmd’
--- re-building ‘Feature_Selection.Rmd’ using rmarkdown
Quitting from Feature_Selection.Rmd:95-117 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'nestedcv'
---
Backtrace:
▆
1. └─base::library(nestedcv)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Feature_Selection.Rmd' failed with diagnostics:
there is no package called 'nestedcv'
--- failed re-building ‘Feature_Selection.Rmd’
SUMMARY: processing the following file failed:
‘Feature_Selection.Rmd’
Error: Vignette re-building failed.
Execution halted
NOTE
r-release-linux-x86_64
Rd cross-references
Unknown package ‘nestedcv’ in Rd xrefs
ERROR
r-release-linux-x86_64
examples
Running examples in ‘multiDEGGs-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiDEGGs_combined_filter
> ### Title: Combined multiDEGGs filter
> ### Aliases: multiDEGGs_combined_filter
>
> ### ** Examples
>
> library(nestedcv)
Error in library(nestedcv) : there is no package called ‘nestedcv’
Execution halted
ERROR
r-release-linux-x86_64
re-building of vignette outputs
Error(s) in re-building vignettes:
...
--- re-building ‘Differential_Network_Analysis.Rmd’ using rmarkdown
--- finished re-building ‘Differential_Network_Analysis.Rmd’
--- re-building ‘Feature_Selection.Rmd’ using rmarkdown
Quitting from Feature_Selection.Rmd:95-117 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'nestedcv'
---
Backtrace:
▆
1. └─base::library(nestedcv)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Feature_Selection.Rmd' failed with diagnostics:
there is no package called 'nestedcv'
--- failed re-building ‘Feature_Selection.Rmd’
SUMMARY: processing the following file failed:
‘Feature_Selection.Rmd’
Error: Vignette re-building failed.
Execution halted
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ERROR 12 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Mar 31, 2026
ERROR
r-devel-linux-x86_64-fedora-clang
Rd cross-references
Unknown package ‘nestedcv’ in Rd xrefs
ERROR
r-devel-linux-x86_64-fedora-gcc
Rd cross-references
Unknown package ‘nestedcv’ in Rd xrefs