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NAME - Static variable in class biolockj.util.ValidationUtil
The first column in an expectation file must be "name"
NAME_PROP - Static variable in class biolockj.module.hello_world.Hello_Friends
NAME_PROP - Static variable in class biolockj.module.hello_world.Step3
NAME_PROP_DEFAULT - Static variable in class biolockj.module.hello_world.Hello_Friends
 
NAME_PROP_DEFAULT - Static variable in class biolockj.module.hello_world.Step3
 
NAME_PROP_DESC - Static variable in class biolockj.module.hello_world.Hello_Friends
 
NAME_PROP_DESC - Static variable in class biolockj.module.hello_world.Step3
 
newSampleRow(String) - Method in class biolockj.module.report.taxa.TaxaLevelTable
 
nextflowLogExists() - Static method in class biolockj.util.NextflowUtil
Return true if the Nextflow log has been saved to the pipeline root directory
NextflowUtil - Class in biolockj.util
This utility builds the Nextflow main.nf used in AWS pipelines.
NextflowUtil() - Constructor for class biolockj.util.NextflowUtil
 
NF_LOG - Static variable in class biolockj.util.NextflowUtil
The Docker container will generate a nextflow.log file in the root directory, this is the file name
NO_BROAD_USE - Static variable in class biolockj.Properties
Added description for general properties that are not meant to be used in their general form.
NO_VERSION - Static variable in interface biolockj.module.BioModule
 
NormalizeByReadsPerMillion - Class in biolockj.module.report.taxa
Normalize each sample for sequencing depth by reporting each value as the number of counts per million counts in a given sample.
NormalizeByReadsPerMillion() - Constructor for class biolockj.module.report.taxa.NormalizeByReadsPerMillion
 
NORMALIZED - Static variable in class biolockj.util.TaxaUtil
File suffix appended to normalized taxa count tables: "norm"
NormalizeTaxaTables - Class in biolockj.module.report.taxa
This utility is used to normalize and/or log-transform the raw OTU counts using the formulas: Normalized OTU count formula = (RC/n)*((SUM(x))/N)+1 Relative abundance formula = Log(log_base) [ (RC/n)*((SUM(x))/N)+1 ] The code implementation supports (log_base = e) and (log_base = 10) which is configured via Constants.REPORT_LOG_BASE property.
NormalizeTaxaTables() - Constructor for class biolockj.module.report.taxa.NormalizeTaxaTables
 
NUM_ITERATIONS - Static variable in class biolockj.module.report.otu.RarefyOtuCounts
Config Positive Integer property "rarefyOtuCounts.iterations" defines the number of iterations to randomly select the "rarefyOtuCounts.quantile"% of OTUs.
NUM_LINES_TEMP_FILE - Static variable in class biolockj.module.implicit.Demultiplexer
Module splits multiplexed file into smaller files with this number of lines: 2000000
NUM_MERGED_READS - Static variable in class biolockj.module.seq.PearMergeReads
Metadata column name for column that holds number of reads per sample after merging: "Num_Merged_Reads"
NUM_META_COLS - Static variable in class biolockj.util.RMetaUtil
Name of R script variable with metadata column count //TODO: is this an int? or a String giving a variable storing an int ?
NUM_OTUS - Static variable in class biolockj.module.implicit.parser.ParserModuleImpl
Metadata column name for column that holds number of OTU hits after any biolockj.module.implicit.parser module executes: "OTU_COUNT"
NUM_RAREFIED_READS - Static variable in class biolockj.module.seq.RarefySeqs
Metadata column name for column that holds number of rarefied reads per sample: "Num_Rarefied_Reads"
NUM_READS - Static variable in class biolockj.module.implicit.RegisterNumReads
Metadata column name for column that holds number of reads per sample: "Num_Reads"
NUM_TRIMMED_READS - Static variable in class biolockj.module.seq.TrimPrimers
Metadata column name for column that holds number of trimmed reads per sample: "Num_Trimmed_Reads"
NUM_VALID_READS - Static variable in class biolockj.module.seq.SeqFileValidator
Column name that holds number of valid reads per sample: "Num_Valid_Reads"
NUMERTIC_TYPE - Static variable in class biolockj.Properties
 
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