Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Includes also utilities for sequence data management under the ACNUC system.
|Author||Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]|
|Date of publication||2016-10-13 20:37:13|
|Maintainer||Simon Penel <email@example.com>|
|License||GPL (>= 2)|
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
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...