ioncopy

Calling Copy Number Alterations in Amplicon Sequencing Data

v2.2.2 · Aug 11, 2020 · GPL-3

Description

Method for the calculation of copy numbers and calling of copy number alterations. The algorithm uses coverage data from amplicon sequencing of a sample cohort as input. The method includes significance assessment, correction for multiple testing and does not depend on normal DNA controls. Budczies (2016 Mar 15) <doi:10.18632/oncotarget.7451>.

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2 NOTE

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Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	29.5s
r-devel-linux-x86_64-debian-gcc	NOTE	21.8s
r-devel-linux-x86_64-fedora-clang	OK	44.8s
r-devel-linux-x86_64-fedora-gcc	OK	39.6s
r-devel-macos-arm64	OK	10s
r-devel-windows-x86_64	OK	49s
r-oldrel-macos-arm64	OK
r-oldrel-macos-x86_64	OK	25s
r-oldrel-windows-x86_64	OK	56s
r-patched-linux-x86_64	OK	26.5s
r-release-linux-x86_64	OK	26.2s
r-release-macos-arm64	OK
r-release-macos-x86_64	OK	32s
r-release-windows-x86_64	OK	49s

Check details (14 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Jan Budczies <jan.budczies@med.uni-heidelberg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jan",
                      family = "Budczies",
                      role = c("aut", "cre"),
                      email = "jan.budczies@med.uni-heidelberg.de"),
               person(given = "Eva",
                      family = "Romanovsky",
                      role = "aut"))
as necessary.

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Jan Budczies <jan.budczies@med.uni-heidelberg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jan",
                      family = "Budczies",
                      role = c("aut", "cre"),
                      email = "jan.budczies@med.uni-heidelberg.de"),
               person(given = "Eva",
                      family = "Romanovsky",
                      role = "aut"))
as necessary.

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OK r-devel-linux-x86_64-fedora-gcc

OK 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

OK r-release-linux-x86_64

OK r-release-macos-arm64

OK r-release-macos-x86_64

OK r-release-windows-x86_64

Check History

NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Jan Budczies <jan.budczies@med.uni-heidelberg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jan",
                      family = "Budczies",
                      role = c("aut", "cre"),
                      email = "jan.budczies@med.uni-heidelberg.de"),
               person(given = "Eva",
                      family = "Romanovsky",
                      role = "aut"))
as necessary.

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Jan Budczies <jan.budczies@med.uni-heidelberg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jan",
                      family = "Budczies",
                      role = c("aut", "cre"),
                      email = "jan.budczies@med.uni-heidelberg.de"),
               person(given = "Eva",
                      family = "Romanovsky",
                      role = "aut"))
as necessary.

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Version History

new 2.2.2 Mar 9, 2026