| bt.annotate | Annotates the depth & breadth of coverage of features from... |
| bt.bamtobed | Converts BAM alignments to BED6 or BEDPE format. |
| bt.bamtofastq | Convert BAM alignments to FASTQ files. |
| bt.bed12tobed6 | Splits BED12 features into discrete BED6 features. |
| bt.bedpetobam | Converts feature records to BAM format. |
| bt.bedtobam | Converts feature records to BAM format. |
| bt.closest | For each feature in A, finds the closest feature (upstream or... |
| bt.cluster | Clusters overlapping/nearby BED/GFF/VCF intervals. |
| bt.complement | Returns the base pair complement of a feature file. |
| bt.coverage | Returns the depth and breadth of coverage of features from B... |
| bt.expand | Replicate lines in a file based on columns of comma-separated... |
| bt.fisher | Calculate Fisher statistic b/w two feature files. |
| bt.flank | Creates flanking interval(s) for each BED/GFF/VCF feature. |
| bt.genomecov | Compute the coverage of a feature file among a genome. |
| bt.getfasta | Extract DNA sequences from a fasta file based on feature... |
| bt.groupby | Summarizes a dataset column based upon common column... |
| bt.igv | Creates a batch script to create IGV images at each interval... |
| bt.intersect | Report overlaps between two feature files. |
| bt.jaccard | Calculate Jaccard statistic b/w two feature files. Jaccard is... |
| bt.links | Creates HTML links to an UCSC Genome Browser from a feature... |
| bt.makewindows | Makes adjacent or sliding windows across a genome or BED... |
| bt.map | Apply a function to a column from B intervals that overlap A. |
| bt.maskfasta | Mask a fasta file based on feature coordinates. |
| bt.merge | Merges overlapping BED/GFF/VCF entries into a single... |
| bt.multicov | Counts sequence coverage for multiple bams at specific loci. |
| bt.multiinter | Identifies common intervals among multiple BED/GFF/VCF files. |
| bt.nuc | Profiles the nucleotide content of intervals in a fasta file. |
| bt.overlap | Computes the amount of overlap (positive values) or distance... |
| bt.pairtobed | Report overlaps between a BEDPE file and a BED/GFF/VCF file. |
| bt.pairtopair | Report overlaps between two paired-end BED files (BEDPE). |
| bt.random | Generate random intervals among a genome. |
| bt.reldist | Calculate the relative distance distribution b/w two feature... |
| bt.sample | Take sample of input file(s) using reservoir sampling... |
| bt.shift | Shift each feature by requested number of base pairs. |
| bt.shuffle | Randomly permute the locations of a feature file among a... |
| bt.slop | Add requested base pairs of "slop" to each feature. |
| bt.sort | Sorts a feature file in various and useful ways. |
| bt.spacing | Report (last col.) the gap lengths between intervals in a... |
| bt.split | Split a Bed file. |
| bt.subtract | Removes the portion(s) of an interval that is overlapped by... |
| bt.summary | Report summary statistics of the intervals in a file |
| bt.tag | Annotates a BAM file based on overlaps with multiple... |
| bt.unionbedg | Combines multiple BedGraph files into a single file, allowing... |
| bt.window | Examines a "window" around each feature in A and reports all... |
| createOptions | Creates options based on user input |
| deleteTempFiles | Deletes temp files |
| establishPaths | Determines if arguments are paths or R objects. Makes temp... |
