Description
A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale. It incorporates two support vector machine models ("precursor" and "mature") trained on publicly available antimicrobial peptide data using calculated physico-chemical and compositional sequence properties described in Meher et al. (2017) <doi:10.1038/srep42362>. In order to support genome-wide analyses, these models are designed to accept any type of protein as input and calculation of compositional properties has been optimised for high-throughput use. For best results it is important to select the model that accurately represents your sequence type: for full length proteins, it is recommended to use the default "precursor" model. The alternative, "mature", model is best suited for mature peptide sequences that represent the final antimicrobial peptide sequence after post-translational processing. For details see Fingerhut et al. (2020) <doi:10.1093/bioinformatics/btaa653>. The 'ampir' package is also available via a Shiny based GUI at <https://ampir.marine-omics.net/>.
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CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| 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 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (2 non-OK)
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
Check History
NOTE 11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
ERROR 10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
package dependencies
Package required but not available: ‘caret’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 2026
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
ERROR 11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
whether package can be installed
Installation failed. See 'd:/Rcompile/CRANpkg/local/4.6/ampir.Rcheck/00install.out' for details.
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 30, 2026
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
ERROR 11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 10, 2026
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
dependencies in R code
Namespace in Imports field not imported from: ‘kernlab’ All declared Imports should be used.
tests
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ampir)
>
> test_check("ampir")
Could not run prediction for 1 proteins because they were either too short or contai
...[truncated]...
is a double vector (0.0237263013580434, 0.0302258304066241, 0.0433991662785352, 0.0393783553576832, 0.618460240944596, ...)
`expected$prob_AMP` is absent
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 82 ]
Error:
! Test failures.
Execution halted