All modules are named with a Biocaml_ prefix to avoid name clashes
with other libraries. For convenience, every module Biocaml_foo is
renamed as Foo under the main Biocaml module. Thus, do
open Biocaml in your code to use the shorter names.
| Biocaml_bam |
Parsing and printing of BAM files.
|
| Biocaml_bar |
Affymetrix's BAR files.
|
| Biocaml_bed |
BED data files.
|
| Biocaml_bpmap |
Affymetrix's BPMAP files.
|
| Biocaml_cel |
Affymetrix's CEL files.
|
| Biocaml_fasta |
FASTA files.
|
| Biocaml_fastq |
FASTQ files.
|
| Biocaml_gff |
GFF files.
|
| Biocaml_jaspar |
Access to Jaspar database
|
| Biocaml_lines |
Manipulate the lines of a file.
|
| Biocaml_mzData |
Read mzData files (mass spectrometry data format).
|
| Biocaml_psl |
PSL files.
|
| Biocaml_sam |
SAM files.
|
| Biocaml_sgr |
Sequence Graph (SGR) files.
|
| Biocaml_track |
Track files in UCSC Genome Browser format.
|
| Biocaml_wig |
WIG data.
|
| Biocaml_zip |
Streaming interface to the Zlib library.
|
Tags classify file types.
| Biocaml_tags |
| Biocaml_entrez |
Entrez Utilities API
|
| Biocaml_accu |
A datastructure (based on Hashtbl) to accumulate values.
|
| Biocaml_genomeMap |
Data structures to represent sets of (possibly annotated) genomic regions
|
| Biocaml_histogram |
Histograms with polymorphic bin types.
|
| Biocaml_interval_tree |
Interval tree (data structure)
|
| Biocaml_range |
Ranges of contiguous integers (integer intervals).
|
| Biocaml_rSet |
Efficient integer sets when many elements expected to be large contiguous sequences of integers.
|
| Biocaml_table |
Generic “tables” (like CSV, TSV, Bed …).
|
| Biocaml_bin_pred |
Performance measurement of binary classifiers.
|
| Biocaml_math |
Numeric mathematics.
|
| Biocaml_pwm |
Position-weight matrix
|
| Biocaml_chr |
Chromosome names.
|
| Biocaml_line |
Single line of text.
|
| Biocaml_strandName |
| Biocaml_about |
General information about this library.
|
| Biocaml_msg |
Consistent printing of errors, warnings, and bugs.
|
| Biocaml_pos |
File positions.
|
| Biocaml_phred_score |
PHRED quality scores.
|
| Biocaml_roman_num |
Roman numerals.
|
| Biocaml_solexa_score |
Solexa quality scores.
|
| Biocaml_transform |
Buffered transforms.
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| Biocaml_sbml |
SBML file parser.
|
| Biocaml_seq |
Nucleic acid sequences.
|
| Biocaml_internal_utils |
Internal utility functions that are commonly needed in many
places.
|
Documentation generated on: Fri Dec 19 19:21:15 UTC 2014
Git commit: d9026a03e89d0ca9162df277544696a3c9579a49