Man pages for anandhupresannan/biostrings
Efficient manipulation of biological strings
| AAString-class | AAString objects |
| AlignedXStringSet-class | AlignedXStringSet and QualityAlignedXStringSet objects |
| align-utils | Utility functions related to sequence alignment |
| AMINO_ACID_CODE | The Single-Letter Amino Acid Code |
| Biostrings-internals | Biostrings internals |
| chartr | Replace letters in a sequence or set of sequences |
| detail | Show (display) detailed object content |
| dinucleotideFrequencyTest | Pearson's chi-squared Test and G-tests for String Position... |
| DNAString-class | DNAString objects |
| findPalindromes | Searching a sequence for palindromes |
| GENETIC_CODE | The Standard Genetic Code and its known variants |
| getSeq | getSeq |
| gregexpr2 | A replacement for R standard gregexpr function |
| HNF4alpha | Known HNF4alpha binding sequences |
| InDel-class | InDel objects |
| injectHardMask | Injecting a hard mask in a sequence |
| IUPAC_CODE_MAP | The IUPAC Extended Genetic Alphabet |
| letter | Subsetting a string |
| letterFrequency | Calculate the frequency of letters in a biological sequence,... |
| longestConsecutive | Obtain the length of the longest substring containing only... |
| lowlevel-matching | Low-level matching functions |
| MaskedXString-class | MaskedXString objects |
| maskMotif | Masking by content (or by position) |
| matchLRPatterns | Find paired matches in a sequence |
| matchPattern | String searching functions |
| matchPDict-exact | Matching a dictionary of patterns against a reference |
| matchPDict-inexact | Inexact matching with matchPDict()/countPDict()/whichPDict() |
| matchProbePair | Find "theoretical amplicons" mapped to a probe pair |
| matchprobes | A function to match a query sequence to the sequences of a... |
| matchPWM | PWM creating, matching, and related utilities |
| match-utils | Utility functions operating on the matches returned by a... |
| MIndex-class | MIndex objects |
| misc | Some miscellaneous stuff |
| MultipleAlignment-class | MultipleAlignment objects |
| needwunsQS | (Deprecated) Needleman-Wunsch Global Alignment |
| nucleotideFrequency | Calculate the frequency of oligonucleotides in a DNA or RNA... |
| padAndClip | Pad and clip strings |
| pairwiseAlignment | Optimal Pairwise Alignment |
| PairwiseAlignments-class | PairwiseAlignments, PairwiseAlignmentsSingleSubject, and... |
| PairwiseAlignments-io | Write a PairwiseAlignments object to a file |
| PDict-class | PDict objects |
| phiX174Phage | Versions of bacteriophage phiX174 complete genome and sample... |
| pid | Percent Sequence Identity |
| pmatchPattern | Longest Common Prefix/Suffix/Substring searching functions |
| QualityScaledXStringSet-class | QualityScaledBStringSet, QualityScaledDNAStringSet,... |
| replaceAt | Extract/replace arbitrary substrings from/in a string or set... |
| replaceLetterAt | Replacing letters in a sequence (or set of sequences) at some... |
| reverseComplement | Sequence reversing and complementing |
| RNAString-class | RNAString objects |
| stringDist | String Distance/Alignment Score Matrix |
| substitution_matrices | Scoring matrices |
| toComplex | Turning a DNA sequence into a vector of complex numbers |
| translate | Translating DNA/RNA sequences |
| trimLRPatterns | Trim Flanking Patterns from Sequences |
| xscat | Concatenate sequences contained in XString, XStringSet and/or... |
| XString-class | BString objects |
| XStringPartialMatches-class | XStringPartialMatches objects |
| XStringQuality-class | PhredQuality, SolexaQuality and IlluminaQuality objects |
| XStringSet-class | XStringSet objects |
| XStringSet-comparison | Comparing and ordering the elements in one or more XStringSet... |
| XStringSet-io | Read/write an XStringSet object from/to a file |
| XStringSetList-class | XStringSetList objects |
| XStringViews-class | The XStringViews class |
| yeastSEQCHR1 | An annotation data file for CHR1 in the yeastSEQ package |
