- seqinr: Biological Sequences Retrieval and Analysis
- lseqinr: To see what's inside the package seqinr
To see what's inside the package seqinr
This is just a shortcut for ls("package:seqinr")
The list of objects in the package seqinr
library(help=seqinr) to have a summary of the functionc available in the package.
- a: Converts amino-acid three-letter code into the one-letter one
- aaa: Converts amino-acid one-letter code into the three-letter one
- aacost: Aerobic cost of amino-acids in Escherichia coli and G+C...
- aaindex: List of 544 physicochemical and biological properties for the...
- AAstat: To Get Some Protein Statistics
- acnucopen: open and close a remote access to an ACNUC database
- al2bp: To Convert a forensic microsatellite allele name into its...
- alllistranks: To get the count of existing lists and all their ranks on...
- amb: Expansion of IUPAC nucleotide symbols
- AnoukResult: Expected numeric results for Ka and Ks computation
- as.alignment: Constructor for class alignment
- as.matrix.alignment: as.matrix.alignment
- autosocket: Returns a socket to the last opened database
- baselineabif: Estimation of baseline value
- bma: Computing an IUPAC nucleotide symbol
- c2s: conversion of a vector of chars into a string
- cai: Codon Adaptation Index
- caitab: Codon Adaptation Index (CAI) w tables
- chargaff: Base composition in ssDNA for 7 bacterial DNA
- choosebank: To select a database structured under ACNUC and located on...
- circle: Draws a circle
- closebank: To close a remote ACNUC database
- clustal: Example of results obtained after a call to read.alignment
- col2alpha: To use a standard color with an alpha transparency chanel
- comp: complements a nucleic acid sequence
- computePI: To Compute the Theoretical Isoelectric Point
- consensus: Consensus and profiles for sequence alignments
- count: Composition of dimer/trimer/etc oligomers
- countfreelists: The number of free lists available and annotation lines in an...
- countsubseqs: Number of subsequences in an ACNUC list
- crelistfromclientdata: To create on server an ACNUC list from data lines sent by...
- dia.bactgensize: Distribution of bacterial genome size from GOLD
- dinucl: Mean zscore on 242 complete bacterial chromosomes
- dist.alignment: Pairwise Distances from Aligned Protein or DNA/RNA Sequences
- dotchart.uco: Cleveland plot for codon usage tables
- dotPlot: Dot Plot Comparison of two sequences
- draw.oriloc: Graphical representation for nucleotide skews in prokaryotic...
- draw.rearranged.oriloc: Graphical representation for rearranged nucleotide skews in...
- draw.recstat: Graphical representation of a recstat analysis.
- ec999: 999 coding sequences from E. coli
- ECH: Forensic Genetic Profile Allelic Ladder Raw Data
- EXP: Vectors of coefficients to compute linear forms.
- extract.breakpoints: Extraction of breakpoint positions on the rearranged...
- extractseqs: To extract the sequences information of a sequence or a list...
- fasta: Example of results obtained after a call to read.alignment
- fastacc: Fast Allele in Common Count
- gb2fasta: Conversion of GenBank file into fasta file
- gbk2g2: Conversion of a GenBank format file into a glimmer-like one
- gbk2g2.euk: Conversion of a GenBank format file into a glimmer-like one....
- GC: Calculates the fractional G+C content of nucleic acid...
- gcO2: GC content and aerobiosis in bacteria
- gcT: GC content and temperature in bacteria
- getAnnot: Generic Function to get sequence annotations
- get.db.growth: Get the exponential growth of nucleic acid database content
- getFrag: Generic function to extract sequence fragments
- getKeyword: Generic function to get keywords associated to sequences
- getLength: Generic function to get the length of sequences
- getlistrank: To get the rank of a list from its name
- getliststate: Asks for information about an ACNUC list of specified rank
- getLocation: Generic function to get the location of subsequences on the...
- getName: Generic function to get the names of sequences
- get.ncbi: Bacterial complete genome data from ncbi ftp site
- getSequence: Generic function to get sequence data
- getTrans: Generic function to translate coding sequences into proteins
- getType: To get available subsequence types in an opened ACNUC...
- gfrag: Extract sequence identified by name or by number from an...
- ghelp: Get help from an ACNUC server
- gs500liz: GS500LIZ size standards
- identifiler: Identifiler allele names
- isenum: Get the ACNUC number of a sequence from its name or accession...
- JLO: Forensic Genetic Profile Raw Data
- kaks: Ka and Ks, also known as dn and ds, computation
- knowndbs: Description of databases known by an ACNUC server
- lseqinr: To see what's inside the package seqinr
- m16j: Fragment of the E. coli chromosome
- mase: Example of results obtained after a call to read.alignment
- modifylist: Modification of an ACNUC list
- move: Rename an R object
- msf: Example of results obtained after a call to read.alignment
- n2s: function to convert the numeric encoding of a DNA sequence...
- oriloc: Prediction of origin and terminus of replication in bacteria.
- parser.socket: Utility function to parse answers from an ACNUC server
- peakabif: Extraction of Peak locations, Heights and Surfaces from ABIF...
- permutation: Sequence permutation according to several different models
- phylip: Example of results obtained after a call to read.alignment
- pK: pK values for the side chain of charged amino acids from...
- plotabif: Electrophoregram plot for ABIF data
- plotladder: Simple plot of an allelic ladder from ABIF data
- plotPanels: Representation of Amplicon Size Ranges of a STR kit.
- plot.SeqAcnucWeb: To Plot Subsequences on the Parent Sequence
- pmw: Protein Molecular Weight
- prepgatannots: Select annotation lines in an ACNUC database
- prettyseq: Text representation of a sequence from an ACNUC server
- print.qaw: Print method for objects from class qaw
- print.SeqAcnucWeb: Print method for objects from class SeqAcnucWeb
- prochlo: Zscore on three strains of Prochlorococcus marinus
- query: To get a list of sequence names from an ACNUC data base...
- read.abif: Read ABIF formatted files
- read.alignment: Read aligned sequence files in mase, clustal, phylip, fasta...
- readBins: Import GenMapper Bins configuration file
- read.fasta: read FASTA formatted files
- readfirstrec: Low level function to get the record count of the specified...
- readPanels: Import GenMapper Panels configuration file
- readsmj: Low level function to read ACNUC SMJYT index files
- rearranged.oriloc: Detection of replication-associated effects on base...
- recstat: Prediction of Coding DNA Sequences.
- residuecount: Total number of residues in an ACNUC list
- revaligntest: Three aligned nucleic acid sequences
- reverse.align: Reverse alignment - from protein sequence alignment to...
- rot13: Ergheaf gur EBG-13 pvcurevat bs n fgevat
- s2c: conversion of a string into a vector of chars
- s2n: simple numerical encoding of a DNA sequence.
- savelist: Save sequence names or accession numbers into a file
- SeqAcnucWeb: Sequence coming from a remote ACNUC data base
- SeqFastaAA: AA sequence in Fasta Format
- SeqFastadna: Class for DNA sequence in Fasta Format
- SeqFrag: Class for sub-sequences
- seqinr-package: Biological Sequences Retrieval and Analysis
- SEQINR.UTIL: utility data for seqinr
- setlistname: Sets the name of an ACNUC list identified by its rank
- splitseq: split a sequence into sub-sequences
- stresc: Utility function to escape LaTeX special characters present...
- stutterabif: Stutter ratio estimation
- swap: Exchange two R objects
- syncodons: Synonymous codons
- synsequence: Random synonymous coding sequence generation
- tablecode: to plot genetic code as in textbooks
- test.co.recstat: Tests if regions located between Stop codons contain putative...
- test.li.recstat: Tests if regions located between Stop codons contain putative...
- toyaa: A toy example of amino-acid counts in three proteins
- toycodon: A toy example of codon counts in three coding sequences
- translate: Translate nucleic acid sequences into proteins
- trimSpace: Trim leading and/or trailing spaces in strings
- uco: Codon usage indices
- ucoweight: Weight of each synonymous codon
- waterabs: Light absorption by the water column
- where.is.this.acc: Scans databases for a given sequence accession number
- words: To get all words from an alphabet.
- words.pos: Positions of possibly degenerated motifs within sequences
- write.fasta: Write sequence(s) into a file in fasta format
- zscore: Statistical over- and under- representation of dinucleotides...