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_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.
Bio::ToolBox - Tools for querying and analysis of genomic data
Bio::ToolBox::Data - Reading, writing, and manipulating data structure
Bio::ToolBox::Data::Feature in lib/Bio/ToolBox/Data.pm
Bio::ToolBox::Data::Iterator in lib/Bio/ToolBox/Data.pm