Documentation
A script to calculate observed vs expected CpG dinucleotides
A program to generate class average summaries for a list of genes or features.
A script to convert bam paired_reads to a gff or bed file.
A script to enumerate Bam alignments or coverage into a wig file.
A script to convert bar files to wig files.
A script to generate GFF3 files for bigwig, bigbed, and bam files.
A script to bin genomic data into windows.
A script will add/remove chromosome name prefixes.
A script to change the order of gene cluster groups in a file.
A script to compare the scores between one or more subfeatures.
A script to convert genomic data between different S cerevisiae versions
A script to calculate correlations between two datasets along the length of a feature.
A script to convert a data file to a bed file.
A script to retrieve sequences from a list of features
A script to convert data into a frequency distribution, useful for graphing.
A script to convert a generic data file to GFF format.
A script to convert a generic data file into a wig file.
A script to filter a Bam file for specific criteria.
A script to find enriched regions in a dataset using a simple threshold.
A script to pull out actual nucleosome fragments and enumerate their sizes.
A script to report the alignment sequence nucleotide frequencies.
A program to collect data for a list of features
A script to retrieve Ensembl annotation and write it out as GFF3.
A script to collect feature information from a BioPerl SeqFeature::Store db.
A script to collect features from a BioPerl SeqFeature::Store database.
A script to collect specific, often un-annotated regions from genes.
A script to pull out overlapping features from the database.
A script to collect data in bins around a relative position.
A script to convert a GFF3 file to a UCSC style refFlat table
A script to graph XY line or dot plots between data sets.
A script to graph a histogram (bar or line) of one or more datasets.
A script to graph Y values along a genomic coordinate X-axis.
A script to identify unique and common SNPs from multiple sequence runs.
A script to intersect two lists of nucleosomes.
A script to join two or more data files and concatenate rows.
A script to locate the position of SNPs and identify codon changes.
A progam to manipulate tab-delimited data files.
A script to map nucleosomes.
A script to assign processed microarray data to genomic coordinates.
A script to associate enriched regions of transcription with gene annotation.
A program to merge two or more data files by appending columns.
A parallelized wrapper program for Novocraft's novoaligner.
A script to print out the available feature types in a database.
A script to quantile normalize two or more raw microarray data sets.
A script to pull out a specific list of data rows from a data file.
A script to run the k-means cluster analysis.
A script to selectively write out paired-end alignments of a given insertion size.
A script to split a data file by rows based on common data values.
A script to convert UCSC gene tables to GFF3 annotation.
A script to verify nucleosome mapping and identify overlaps.
A script to convert a text wiggle file to a tab-delimited text file.
Modules
Tools for querying and analysis of genomic data
Reading, writing, and manipulating data structure
Provides
in lib/Bio/ToolBox/Data.pm
in lib/Bio/ToolBox/Data.pm