SeqFeatR
A Tool to Associate FASTA Sequences and Features
Description
Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses, see Budeus (2016) <doi:10.1371/journal.pone.0146409>.
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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 | NOTE |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-macos-arm64 | NOTE |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | ERROR |
| 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 | ERROR |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (14 non-OK)
package dependencies
Package required but not available: ‘Biostrings’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
R code for possible problems
find_possible_epitopes_inner: no visible global function definition for ‘stringDist’ Undefined global functions or variables: stringDist
R code for possible problems
find_possible_epitopes_inner: no visible global function definition for ‘stringDist’ Undefined global functions or variables: stringDist
R code for possible problems
find_possible_epitopes_inner: no visible global function definition for ‘stringDist’ Undefined global functions or variables: stringDist
R code for possible problems
find_possible_epitopes_inner: no visible global function definition for ‘stringDist’ Undefined global functions or variables: stringDist
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package dependencies
Package required but not available: ‘widgetTools’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
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package dependencies
Package required but not available: ‘widgetTools’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
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Check History
ERROR 7 OK · 4 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE Mar 9, 2026
package dependencies
Package required but not available: ‘Biostrings’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
R code for possible problems
find_possible_epitopes_inner: no visible global function definition for ‘stringDist’ Undefined global functions or variables: stringDist
R code for possible problems
find_possible_epitopes_inner: no visible global function definition for ‘stringDist’ Undefined global functions or variables: stringDist
R code for possible problems
find_possible_epitopes_inner: no visible global function definition for ‘stringDist’ Undefined global functions or variables: stringDist
R code for possible problems
find_possible_epitopes_inner: no visible global function definition for ‘stringDist’ Undefined global functions or variables: stringDist
package dependencies
Package required but not available: ‘widgetTools’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘widgetTools’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.