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Index of modules


A
About [Biocaml]
Accu [Biocaml]
Arg [Biocaml_internal_pervasives]
Array [Biocaml_internal_pervasives]

B
Backtrace [Biocaml_internal_pervasives]
Bag [Biocaml_internal_pervasives]
Bam [Biocaml]
Bar [Biocaml]
Bed [Biocaml]
Big_int [Biocaml_internal_pervasives]
Bigbuffer [Biocaml_internal_pervasives]
Bigstring [Biocaml_internal_pervasives]
Bigsubstring [Biocaml_internal_pervasives]
Bin_prot [Biocaml_internal_pervasives]
Binary_packing [Biocaml_internal_pervasives]
Biocaml
Biocaml_about
Version string of the library: "0.2.0"
Biocaml_accu
A datastructure (based on Hashtbl) to accumulate values.
Biocaml_bam
0-based, -1 if undefined
Biocaml_bar
Affymetrix's BAR files.
Biocaml_bed
BED data.
Biocaml_bpmap
Affymetrix's BPMAP files.
Biocaml_cel
Affymetrix's CEL files.
Biocaml_chrName
Chromosome names.
Biocaml_entrez
Entrez Utilities API
Biocaml_fasta
FASTA files.
Biocaml_fastq
FASTQ data.
Biocaml_genomeMap
Indicator function on a genome
Biocaml_gff
GFF files.
Biocaml_histogram
Histograms with polymorphic bin types.
Biocaml_internal_pervasives
Internal "standard" library.
Biocaml_interval_tree
Interval tree (data structure)
Biocaml_iset
DIET : Discrete Interval Encoding Trees
Biocaml_jaspar
Biocaml_line
Single line of text.
Biocaml_lines
Lines of a file.
Biocaml_math
Numeric mathematics.
Biocaml_msg
Consistent printing of errors, warnings, and bugs.
Biocaml_mzData
Read mzData files (mass spectrometry data format).
Biocaml_phred_score
PHRED quality scores.
Biocaml_pos
File positions.
Biocaml_pwm
Position-weight matrix
Biocaml_rSet
Efficient integer sets when many elements expected to be large contiguous sequences of integers.
Biocaml_range
Ranges of contiguous integers (integer intervals).
Biocaml_roc
Performance measurement for binary classification.
Biocaml_romanNum
Roman numerals.
Biocaml_sam
SAM files.
Biocaml_sbml
SBML file parser.
Biocaml_seq
Nucleic acid sequences.
Biocaml_sgr
Sequence Graph (SGR) files.
Biocaml_solexa_score
Solexa quality scores.
Biocaml_strandName
Strand names.
Biocaml_stream
This module is an enhancement of the stdlib's Stream module.
Biocaml_streamable
A signature for data structures that may be converted to and from a Stream.t.
Biocaml_table
Generic "tables" (like CSV, TSV, Bed ...).
Biocaml_tags
Biocaml_track
Track files in UCSC Genome Browser format.
Biocaml_transcripts
Transcripts are integer intervals containing a list of exons.
Biocaml_transform
Buffered transforms.
Biocaml_wig
WIG data.
Biocaml_zip
Streaming interface to the Zlib library.
Bool [Biocaml_internal_pervasives]
Bpmap [Biocaml]
Buffer [Biocaml_internal_pervasives]
Buffer [Biocaml_lines]
Buffer of lines.

C
Caml [Biocaml_internal_pervasives]
Cel [Biocaml]
Char [Biocaml_internal_pervasives]
ChrName [Biocaml]
Command [Biocaml_internal_pervasives]
Counter [Biocaml_accu]

D
Dbtag [Biocaml_entrez.Make]
Debug [Biocaml_internal_pervasives]
Dequeue [Biocaml_internal_pervasives]

E
Entrez [Biocaml]
Error [Biocaml_sam]
Error [Biocaml_lines]
Errors.
Error [Biocaml_fastq]
Error [Biocaml_fasta]
Errors.
Error [Biocaml_bed]
Exceptionful [Biocaml_fastq]
Exn [Biocaml_internal_pervasives]

F
Fasta [Biocaml]
Fastq [Biocaml]
Filename [Biocaml_internal_pervasives]
Flags [Biocaml_sam]
Float [Biocaml_internal_pervasives]
Fn [Biocaml_internal_pervasives]

G
Gene [Biocaml_entrez.Make]
Gene_ref [Biocaml_entrez.Make]
GenomeMap [Biocaml]
Gff [Biocaml]

H
Hashtbl [Biocaml_internal_pervasives]
Histogram [Biocaml]

I
In_channel [Biocaml_internal_pervasives]
Infix [Biocaml_stream]
Int [Biocaml_internal_pervasives]
Int32 [Biocaml_internal_pervasives]
Int63 [Biocaml_internal_pervasives]
Int64 [Biocaml_internal_pervasives]
Interfaces [Biocaml_internal_pervasives]
Interval [Biocaml_internal_pervasives]
Interval_tree [Biocaml]

J
Jaspar [Biocaml]

L
LMap [Biocaml_genomeMap]
A set of locations with an attached value on each of them
LSet [Biocaml_genomeMap]
A set of locations
Lazy [Biocaml_internal_pervasives]
Line [Biocaml]
Line_oriented [Biocaml_transform]
A buffering parsing_buffer for line-oriented formats.
Lines [Biocaml]
List [Biocaml_internal_pervasives]
Low_level_parsing [Biocaml_sam]

M
Make [Biocaml_entrez]
Map [Biocaml_internal_pervasives]
Math [Biocaml]
Monad [Biocaml_internal_pervasives]
Msg [Biocaml]
MzData [Biocaml]

N
Nat [Biocaml_internal_pervasives]
Nativeint [Biocaml_internal_pervasives]
Num [Biocaml_internal_pervasives]

O
Object_id [Biocaml_entrez.Make]
Option [Biocaml_internal_pervasives]
Order [Biocaml_internal_pervasives]
Out_channel [Biocaml_internal_pervasives]

P
Parse [Biocaml_internal_pervasives]
Utility functions to write manual parsers.
Phred_score [Biocaml]
Pos [Biocaml]
Precursor [Biocaml_mzData]
Printer_queue [Biocaml_transform]
A generic buffering printer.
Printexc [Biocaml_internal_pervasives]
Printf [Biocaml_internal_pervasives]
Pubmed [Biocaml_entrez.Make]
PubmedSummary [Biocaml_entrez.Make]
Pwm [Biocaml]

Q
Queue [Biocaml_internal_pervasives]

R
RSet [Biocaml]
Random [Biocaml_internal_pervasives]
Range [Biocaml]
Ratio [Biocaml_internal_pervasives]
Relation [Biocaml_accu]
Result [Biocaml_internal_pervasives]
Result [Biocaml_fasta]
Roc [Biocaml]
RomanNum [Biocaml]
Row [Biocaml_table]
Definition of rows

S
Sam [Biocaml]
Sbml [Biocaml]
Selection [Biocaml_genomeMap]
Indicator function on a genome
Seq [Biocaml]
Set [Biocaml_internal_pervasives]
Sgr [Biocaml]
Solexa_score [Biocaml]
Stack [Biocaml_internal_pervasives]
StrandName [Biocaml]
Stream [Biocaml_internal_pervasives]
Stream [Biocaml]
Streamable [Biocaml_internal_pervasives]
Streamable [Biocaml]
String [Biocaml_internal_pervasives]
Sys [Biocaml_internal_pervasives]

T
Table [Biocaml]
Tags [Biocaml]
Time [Biocaml_internal_pervasives]
Track [Biocaml]
Transform [Biocaml_zip]
Transform [Biocaml_wig]
Transform [Biocaml]
Transform [Biocaml_track]
Low-level transforms.
Transform [Biocaml_sam]
Transform [Biocaml_lines]
Transform [Biocaml_gff]
Transform [Biocaml_fastq]
Transform [Biocaml_fasta]
Low-level transforms.
Transform [Biocaml_bed]
Transform [Biocaml_bam]
Tree [Biocaml_msg]
Message tree for more complex messages.

U
Url [Biocaml_internal_pervasives]
Operations on URL-style encodings.

W
Wig [Biocaml]

Z
Zip [Biocaml]

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