align-utils |
Utility functions related to sequence alignment |
aligned |
AlignedXStringSet and QualityAlignedXStringSet objects |
aligned-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
aligned-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
alignedPattern |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
alignedPattern-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
alignedSubject |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
alignedSubject-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
AlignedXStringSet |
AlignedXStringSet and QualityAlignedXStringSet objects |
AlignedXStringSet-class |
AlignedXStringSet and QualityAlignedXStringSet objects |
AlignedXStringSet0 |
AlignedXStringSet and QualityAlignedXStringSet objects |
AlignedXStringSet0-class |
AlignedXStringSet and QualityAlignedXStringSet objects |
as.character-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
as.character-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
as.matrix-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
nchar-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
nchar-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
nedit |
Utility functions related to sequence alignment |
nedit-method |
Utility functions related to sequence alignment |
nindel |
AlignedXStringSet and QualityAlignedXStringSet objects |
nindel-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
nindel-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
nmatch-method |
Utility functions related to sequence alignment |
nmismatch-method |
Utility functions related to sequence alignment |
nucleotideSubstitutionMatrix |
Utilities to generate substitution matrices |
pairwiseAlignment |
Optimal Pairwise Alignment |
pairwiseAlignment-method |
Optimal Pairwise Alignment |
PairwiseAlignments |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
PairwiseAlignments-class |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
PairwiseAlignments-io |
Write a PairwiseAlignments object to a file |
PairwiseAlignments-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
PairwiseAlignmentsSingleSubject |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
PairwiseAlignmentsSingleSubject-class |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
PairwiseAlignmentsSingleSubject-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
PairwiseAlignmentsSingleSubjectSummary |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
PairwiseAlignmentsSingleSubjectSummary-class |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
PAM120 |
Predefined scoring matrices |
PAM250 |
Predefined scoring matrices |
PAM30 |
Predefined scoring matrices |
PAM40 |
Predefined scoring matrices |
PAM70 |
Predefined scoring matrices |
parallelVectorNames-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
parallel_slot_names-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
parallel_slot_names-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
pattern-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
phiX174Phage |
Versions of bacteriophage phiX174 complete genome and sample short reads |
pid |
Percent Sequence Identity |
pid-method |
Percent Sequence Identity |
predefined_scoring_matrices |
Predefined scoring matrices |
score-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
seqtype-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
seqtype-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
show-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
show-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
srPhiX174 |
Versions of bacteriophage phiX174 complete genome and sample short reads |
start-method |
AlignedXStringSet and QualityAlignedXStringSet objects |
stringDist |
String Distance/Alignment Score Matrix |
stringDist-method |
String Distance/Alignment Score Matrix |
subject-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |
substitution_matrices |
Utilities to generate substitution matrices |
summary-method |
PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects |