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.
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Biocaml_bar |
Affymetrix's BAR files.
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Biocaml_bed |
BED data files.
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Biocaml_bpmap |
Affymetrix's BPMAP files.
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Biocaml_cel |
Affymetrix's CEL files.
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Biocaml_fasta |
FASTA files.
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Biocaml_fastq |
FASTQ data.
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Biocaml_gff |
GFF files.
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Biocaml_jaspar |
Jaspar data.
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Biocaml_lines |
Manipulate the lines of a file.
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Biocaml_mzData |
Read mzData files (mass spectrometry data format).
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Biocaml_psl |
PSL files.
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Biocaml_sam |
SAM files and SAM-alignements high-level representation.
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Biocaml_sgr |
Sequence Graph (SGR) files.
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Biocaml_track |
Track files in UCSC Genome Browser format.
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Biocaml_wig |
WIG data.
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Biocaml_zip |
Streaming interface to the Zlib library.
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Tags classify file types.
Biocaml_tags |
Meta-information about files and their formats.
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Biocaml_entrez |
Entrez Utilities API
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Biocaml_accu |
A datastructure (based on Hashtbl) to accumulate values.
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Biocaml_genomeMap |
Indicator function on a genome
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Biocaml_histogram |
Histograms with polymorphic bin types.
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Biocaml_interval_tree |
Interval tree (data structure)
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Biocaml_range |
Ranges of contiguous integers (integer intervals).
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Biocaml_rSet |
Efficient integer sets when many elements expected to be large contiguous sequences of integers.
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Biocaml_table |
Generic “tables” (like CSV, TSV, Bed …).
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Biocaml_math |
Numeric mathematics.
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Biocaml_pwm |
Position-weight matrix
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Biocaml_roc |
Performance measurement for binary classification.
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Biocaml_chr |
Chromosome names.
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Biocaml_line |
Single line of text.
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Biocaml_strandName |
Strand names.
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Biocaml_about |
Version string of the library:
"0.3.1"
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Biocaml_msg |
Consistent printing of errors, warnings, and bugs.
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Biocaml_pos |
File positions.
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Biocaml_phred_score |
PHRED quality scores.
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Biocaml_romanNum |
Roman numerals.
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Biocaml_solexa_score |
Solexa quality scores.
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Biocaml_transform |
Buffered transforms.
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Biocaml_sbml |
SBML file parser.
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Biocaml_seq |
Nucleic acid sequences.
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Biocaml_internal_pervasives |
Internal "standard" library.
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