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Bio-ToolBox-1.19
River stage zero No dependents
4 ++

Documentation

CpG_calculator.pl
A script to calculate observed vs expected CpG dinucleotides
average_gene.pl
A program to generate class average summaries for a list of features.
bam2gff_bed.pl
A script to convert bam paired_reads to a gff or bed file.
bam2wig.pl
A script to enumerate Bam alignments or coverage into a wig file.
bar2wig.pl
A script to convert bar files to wig files.
big_file2gff3.pl
A script to generate GFF3 files for bigwig, bigbed, and bam files.
bin_genomic_data.pl
A script to bin genomic data into windows.
change_chr_prefix.pl
A script will add/remove chromosome name prefixes.
change_cluster_order.pl
A script to change the order of gene cluster groups in a file.
compare_subfeature_scores.pl
A script to compare the scores between one or more subfeatures.
convert_yeast_genome_version.pl
A script to convert genomic data between different S cerevisiae versions
correlate_position_data.pl
A script to calculate correlations between two datasets along the length of a feature.
data2bed.pl
A script to convert a data file to a bed file.
data2fasta.pl
A script to retrieve sequences from a list of features
data2gff.pl
A script to convert data into a frequency distribution, useful for graphing.
data2gff.pl
A script to convert a generic data file to GFF format.
data2wig.pl
A script to convert a generic data file into a wig file.
db_setup.pl
db_types.pl
A script to print out the available feature types in a database.
filter_bam.pl
A script to filter a Bam file for specific criteria.
find_enriched_regions.pl
A script to find enriched regions in a dataset using a simple threshold.
get_actual_nuc_sizes.pl
A script to pull out actual nucleosome fragments and enumerate their sizes.
get_bam_seq_stats.pl
A script to report the alignment sequence nucleotide frequencies.
get_datasets.pl
A program to collect data for a list of features
get_ensembl_annotation.pl
A script to retrieve Ensembl annotation and write it out as GFF3.
get_feature_info.pl
A script to collect feature information from a BioPerl SeqFeature::Store db.
get_features.pl
A script to collect features from a BioPerl SeqFeature::Store database.
get_gene_regions.pl
A script to collect specific, often un-annotated regions from genes.
get_intersecting_features.pl
A script to pull out overlapping features from the database.
get_relative_data.pl
A script to collect data in bins around a relative position.
gff3_to_ucsc_table.pl
A script to convert a GFF3 file to a UCSC style refFlat table
graph_data.pl
A script to graph XY line or dot plots between data sets.
graph_histogram.pl
A script to graph a histogram (bar or line) of one or more datasets.
graph_profile.pl
A script to graph Y values along a genomic coordinate X-axis.
intersect_SNPs.pl
A script to identify unique and common SNPs from multiple sequence runs.
intersect_nucs.pl
A script to intersect two lists of nucleosomes.
join_data_file.pl
A script to join two or more data files and concatenate rows.
locate_SNPs.pl
A script to locate the position of SNPs and identify codon changes.
manipulate_datasets.pl
A progam to manipulate tab-delimited data files.
map_nucleosomes.pl
A script to map nucleosomes.
map_oligo_data2gff.pl
A script to assign processed microarray data to genomic coordinates.
map_transcripts.pl
A script to associate enriched regions of transcription with gene annotation.
merge_datasets.pl
A program to merge two or more data files by appending columns.
novo_wrapper.pl
A parallelized wrapper program for Novocraft's novoaligner.
process_microarray.pl
A script to quantile normalize two or more raw microarray data sets.
pull_features.pl
A script to pull out a specific list of data rows from a data file.
run_cluster.pl
A script to run the k-means cluster analysis.
split_bam_by_isize.pl
A script to selectively write out paired-end alignments of a given insertion size.
split_data_file.pl
A script to split a data file by rows based on common data values.
ucsc_table2gff3.pl
A script to convert UCSC gene tables to GFF3 annotation.
verify_nucleosome_mapping.pl
A script to verify nucleosome mapping and identify overlaps.
wig2data.pl
A script to convert a text wiggle file to a tab-delimited text file.

Modules

Bio::ToolBox
Tools for querying and analysis of genomic data
Bio::ToolBox::Data
Reading, writing, and manipulating data structure
Bio::ToolBox::big_helper
Bio::ToolBox::data_helper
Bio::ToolBox::db_helper
Bio::ToolBox::db_helper::bam
Bio::ToolBox::db_helper::bigbed
Bio::ToolBox::db_helper::bigwig
Bio::ToolBox::db_helper::config
Bio::ToolBox::db_helper::gff3_parser
Bio::ToolBox::db_helper::useq
Bio::ToolBox::db_helper::wiggle
Bio::ToolBox::file_helper

Provides

Bio::ToolBox::Data::Feature
in lib/Bio/ToolBox/Data.pm
Bio::ToolBox::Data::Iterator
in lib/Bio/ToolBox/Data.pm

Other files