N-Index

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All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

N

NAME_Deviation - Static variable in class bacnet.datamodel.dataset.EGDeWTdata
NAME_Mean - Static variable in class bacnet.datamodel.dataset.EGDeWTdata
NavigationManagement - Class in bacnet.raprcp: Every lmethods for managing navigation state in eclipse.rap application.
NavigationManagement() - Constructor for class bacnet.raprcp.NavigationManagement
NBRF - Enum constant in enum org.biojava3.core.sequence.DataSource
NCBI - Enum constant in enum org.biojava3.core.sequence.DataSource
NCBIFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> - Class in bacnet.reader: My own implementation of a FastaHeaderParserInterface to parse Fasta files from NCBI ftp NCBI fna (genome and plasmids) gi|gi-number|ref|accession|name gi|16802048|ref|NC_003210.1| Listeria monocytogenes EGD-e, complete genome NCBI ffn (coding) ref|refGenome gi-number|:start-end name ref|NC_003210.1|:318-1673 chromosomal replication initiation protein [Listeria monocytogenes EGD-e] NCBI frn (non-coding) ref|refGenome gi-number|:start-end| name| [locus-tag] ref|NC_003210|:82705-82777|Lys tRNA| [locus_tag=lmot01] NCBI faa (proteins) gi|gi-number|ref|accession|name gi|16802049|ref|NP_463534.1| chromosomal replication initiation protein [Listeria monocytogenes EGD-e]
NCBIFastaHeaderParser() - Constructor for class bacnet.reader.NCBIFastaHeaderParser
NcRNA - Class in bacnet.datamodel.sequence
NcRNA - Enum constant in enum bacnet.datamodel.sequence.Sequence.SeqType
NcRNA() - Constructor for class bacnet.datamodel.sequence.NcRNA
NcRNA(String, int, int, char) - Constructor for class bacnet.datamodel.sequence.NcRNA
NcRNA.TypeNcRNA - Enum in bacnet.datamodel.sequence
NEGATIVE - Enum constant in enum org.biojava3.core.sequence.Strand
Network - Class in bacnet.datamodel.dataset: Network object for co-expression network analysis and visualisation
Network() - Constructor for class bacnet.datamodel.dataset.Network
NETWORK - Static variable in class bacnet.utils.HTMLUtils
NetworkCreation - Class in bacnet.scripts.database
NetworkCreation() - Constructor for class bacnet.scripts.database.NetworkCreation
NewLocusTagArray - Static variable in class bacnet.datamodel.annotation.LocusTag
newNucleotideCompound(String, String, String...) - Method in class org.biojava3.core.sequence.compound.DNACompoundSet
newNucleotideCompound(String, String, String...) - Method in class org.biojava3.core.sequence.compound.RNACompoundSet
next() - Method in class org.biojava3.core.sequence.template.SequenceMixin.SequenceIterator
next() - Method in class org.biojava3.genome.parsers.gff.LocIterator: Get next window of default size, then increment position by default amount.
next(int, int) - Method in class org.biojava3.genome.parsers.gff.LocIterator: Get next window of specified size, then increment position by specified amount.
NGS - Class in bacnet.datamodel.dataset: Class for manipulating various RNASeq data, herited from ExpressionData
double[] value is of genome size, when ones want to see RNAseq expression at a certain bp position, just extract values[bpposition]
Need to be loaded first, and unlog has RNASeq will be logged for display when convert in the platform
NGS() - Constructor for class bacnet.datamodel.dataset.NGS
NGS(String, String) - Constructor for class bacnet.datamodel.dataset.NGS
NGSCreation - Class in bacnet.scripts.database
NGSCreation() - Constructor for class bacnet.scripts.database.NGSCreation
NH2 - Enum constant in enum bacnet.datamodel.proteomics.NTerm.TypeModif
NimbleGen - Class in bacnet.scripts.listeriomics.technology
NimbleGen() - Constructor for class bacnet.scripts.listeriomics.technology.NimbleGen
nonOverlappingKmers(Sequence<C>, int) - Static method in class org.biojava3.core.sequence.template.SequenceMixin: Produces kmers of the specified size e.g.
norm(ExpressionMatrix) - Static method in class bacnet.scripts.core.normalization.MedianNormalization: For each column of the ExpressionMatrix, delete the median.
norm(ExpressionMatrix, String) - Static method in class bacnet.scripts.core.normalization.MedianNormalization: Normalize by median the column with a specific name
norm(ExpressionMatrix, String) - Static method in class bacnet.scripts.core.normalization.VarianceNormalization: Normalize by variance the column with a specific name
Multiply each value by Math.sqr(1/var(x))
norm(Experiment) - Static method in class bacnet.scripts.core.normalization.GENormalization
norm(Experiment) - Static method in class bacnet.scripts.core.normalization.GRNormalization: Normalize the Tiling contained in the Experiment
Run one thread for each bioCondition
The number of thread is limited by the number of processor

It runs DNA reference normalization (Hubert et al.), it can uses also an additional reference data for normalization (indicates by boolean normalization).
normalize(String, String) - Static method in class bacnet.scripts.listeriomics.technology.Macroarray: Data are not Log transformed:
add the min value to be sure to have only positive values log2 transform
normalize(String, String) - Static method in class bacnet.scripts.listeriomics.technology.NimbleGen: Data are not Log transformed:
add the min value to be sure to have only positive values log2 transform
normalize(String, String, String) - Static method in class bacnet.scripts.listeriomics.technology.Agilent: Data are not Log transformed:
add the min value to be sure to have only positive values log2 transform
normalizeCountFiles(Experiment) - Static method in class bacnet.scripts.database.NGSCreation: ConvertCountFile and add them to the database
normGE(ExpressionMatrix) - Static method in class bacnet.scripts.core.normalization.MedianNormalization: From a GE ExpressionMatrix containing 5 columns (3replicates exp + median + stdev) Apply median normalization to the first 3 columns, and recalculate median and stdev
normGE(Experiment) - Static method in class bacnet.scripts.core.normalization.MedianNormalization
normTiling(Experiment) - Static method in class bacnet.scripts.core.normalization.MedianNormalization: Load all TilingData in this Experiment and normalize by the median, and save in the Tiling/MedianNorm path
NOTFOUND_LOCUSTAG_CHANGE_PATH - Static variable in class bacnet.scripts.listeriomics.PhylogenyListeriomics
NTerm - Class in bacnet.datamodel.proteomics: Object for managing every mapped sequences
NTerm - Enum constant in enum bacnet.datamodel.dataset.OmicsData.TypeData
NTerm() - Constructor for class bacnet.datamodel.proteomics.NTerm
NTerm(String, int, int, char) - Constructor for class bacnet.datamodel.proteomics.NTerm
NTERM_PROJECT_BHI - Static variable in class bacnet.datamodel.proteomics.NTerm
NTerm.ExperimentName - Enum in bacnet.datamodel.proteomics
NTerm.MappingFrame - Enum in bacnet.datamodel.proteomics
NTerm.TypeModif - Enum in bacnet.datamodel.proteomics: Type of modification at the start of a peptide
NTermConservationWithRiboProfiling - Class in bacnet.scripts.listeriomics.nterm: Run different method to compare iTIS position (internal translation) to data of Ribosome profiling in Bacillus and Ecoli:
compare the gene by BlastN find internal translation in the ribosome profiling find internal SD sequence
NTermConservationWithRiboProfiling() - Constructor for class bacnet.scripts.listeriomics.nterm.NTermConservationWithRiboProfiling
NTermCreateData - Class in bacnet.datamodel.proteomics: Transform excel table describing all N-Terminal peptides found in Listeria
Find the position of each peptide in Listeria genome create a NGS data from it
NTermCreateData(Genome) - Constructor for class bacnet.datamodel.proteomics.NTermCreateData: Initialize a void NTermCreateData object and run initializeGenomeSequence() to have the genome on the six frames
NTermCreateData(String, String) - Constructor for class bacnet.datamodel.proteomics.NTermCreateData: Create table summarizing the data
Curate the table by adding different information
Create streaming data for the viewer
Run Mapping and creation of summary tables
mapPeptide();
curateTable();

Create all NTerm from the table
createNTermExperiment();
NTermCreation.findStart(nameNTermData);
NTermCreation.findTSS(nameNTermData);
NTermCreation.findCodonUsage(nameNTermData);
NTermCreation.findSDSequence(nameNTermData);

Complete NTermExp by creating all HashMaps
NTermData nTermExp = NTermData.load(nameNTermData);
nTermExp.createHashMap();
nTermExp.createGeneHashMap();
nTermExp.createProteolyseMap();
nTermExp.createAnnotation();
nTermExp.save();
NTermCreateFinalData - Class in bacnet.scripts.listeriomics.nterm: Genertal class for creation of NTerminomics tables
NTermCreateFinalData(String, String) - Constructor for class bacnet.scripts.listeriomics.nterm.NTermCreateFinalData: From the list created by Francis, update all Nterm peptides, indicating which type of TIS (translation initiation sites) they are: annotated TIS multiple TIS updated TIS internal TIS
NTermData - Class in bacnet.datamodel.dataset
NTermData() - Constructor for class bacnet.datamodel.dataset.NTermData
NTermData(String) - Constructor for class bacnet.datamodel.dataset.NTermData
NTermData(String, HashMap<String, NTerm>) - Constructor for class bacnet.datamodel.dataset.NTermData
NTermDatabase - Class in bacnet.scripts.listeriomics.nterm
NTermDatabase() - Constructor for class bacnet.scripts.listeriomics.nterm.NTermDatabase
NTermFilter - Class in bacnet.datamodel.proteomics
NTermFilter(NTermData, String) - Constructor for class bacnet.datamodel.proteomics.NTermFilter: Filter a NTermData using the table of filter found in fileName
NTerminomicsView - Class in bacnet.genomeBrowser
NTerminomicsView() - Constructor for class bacnet.genomeBrowser.NTerminomicsView
NTermMain - Class in bacnet.scripts.listeriomics.nterm: General method for running all methods related to NTerm project
NTermMain() - Constructor for class bacnet.scripts.listeriomics.nterm.NTermMain
NTermStat - Class in bacnet.scripts.listeriomics.nterm: List of method to do statistics about common features in N-Terminus of genes: - start codon - SD binding - AU proportion - Folding energy
NTermStat() - Constructor for class bacnet.scripts.listeriomics.nterm.NTermStat
NTermStatProteolyse - Class in bacnet.scripts.listeriomics.nterm: A list of methods to assess the quantity of proteolysis on the peptides
NTermStatProteolyse() - Constructor for class bacnet.scripts.listeriomics.nterm.NTermStatProteolyse
NTermSummaryTable - Class in bacnet.datamodel.proteomics: List of methods for creating Summary Table for TIS
Using NTermFilter we have regroup TIS in different overlap groups, which we use now to create the Summary Tables.
NTermSummaryTable() - Constructor for class bacnet.datamodel.proteomics.NTermSummaryTable
NTermTranscriptome - Class in bacnet.scripts.listeriomics.nterm
NTermTranscriptome() - Constructor for class bacnet.scripts.listeriomics.nterm.NTermTranscriptome
NTermUtils - Class in bacnet.datamodel.proteomics
NTermUtils() - Constructor for class bacnet.datamodel.proteomics.NTermUtils
NucleotideCompound - Class in org.biojava3.core.sequence.compound
NucleotideCompound(String, CompoundSet<NucleotideCompound>, String) - Constructor for class org.biojava3.core.sequence.compound.NucleotideCompound
NucleotideCompound(String, CompoundSet<NucleotideCompound>, String, NucleotideCompound[]) - Constructor for class org.biojava3.core.sequence.compound.NucleotideCompound

A B C D E F G H I J L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form