A | |
| About [Biocaml] | |
| Accu [Biocaml] | |
| Alignment0 [Biocaml_bam_alt] |
Representation of partially parsed alignments.
|
| Array [Biocaml_internal_utils] | |
B | |
| Bam [Biocaml] | |
| Bam_alt [Biocaml] | |
| Bar [Biocaml] | |
| Bed [Biocaml] | |
| Bin_pred [Biocaml] | |
| Biocaml | |
| Biocaml_about |
General information about this library.
|
| Biocaml_accu |
A datastructure (based on Hashtbl) to accumulate values.
|
| Biocaml_bam |
Parsing and printing of BAM files.
|
| Biocaml_bam_alt |
Read and write BAM format.
|
| Biocaml_bar |
Affymetrix's BAR files.
|
| Biocaml_bed |
BED data files.
|
| Biocaml_bgzf |
I/O on Blocked GNU Zip format (BGZF) files
|
| Biocaml_bin_pred |
Performance measurement of binary classifiers.
|
| Biocaml_bpmap |
Affymetrix's BPMAP files.
|
| Biocaml_cel |
Affymetrix's CEL files.
|
| Biocaml_chr |
Chromosome names.
|
| Biocaml_entrez |
Entrez Utilities API
|
| Biocaml_fasta |
FASTA files.
|
| Biocaml_fastq |
FASTQ files.
|
| Biocaml_genomeMap |
Data structures to represent sets of (possibly annotated) genomic regions
|
| Biocaml_gff |
GFF files.
|
| Biocaml_histogram |
Histograms with polymorphic bin types.
|
| Biocaml_internal_utils |
Internal utility functions that are commonly needed in many
places.
|
| Biocaml_interval_tree |
Interval tree (data structure)
|
| Biocaml_iset |
DIET : Discrete Interval Encoding Trees
|
| Biocaml_jaspar |
Access to Jaspar database
|
| Biocaml_line |
Single line of text.
|
| Biocaml_lines |
Manipulate the 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_psl |
PSL files.
|
| 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_roman_num |
Roman numerals.
|
| Biocaml_sam |
SAM files.
|
| Biocaml_sam_deprecated |
SAM files and SAM-alignements high-level representation.
|
| Biocaml_sbml |
SBML file parser.
|
| Biocaml_seq |
Nucleic acid sequences.
|
| Biocaml_seq_range |
Range on a sequence, where the sequence is represented by an identifier.
|
| Biocaml_sgr |
Sequence Graph (SGR) files.
|
| Biocaml_solexa_score |
Solexa quality scores.
|
| Biocaml_strand |
Strand names.
|
| Biocaml_table |
Generic “tables” (like CSV, TSV, Bed …).
|
| 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_vcf |
Parsing of VCF files.
|
| Biocaml_wig |
WIG data.
|
| Biocaml_zip |
Streaming interface to the Zlib library.
|
| Bpmap [Biocaml] | |
| Buffer [Biocaml_lines] | |
C | |
| Cel [Biocaml] | |
| Chr [Biocaml] | |
| Counter [Biocaml_accu] | |
D | |
| Dbtag [Biocaml_entrez.Make] | |
| Debug [Biocaml_internal_utils] | |
| Default [Biocaml_zip] | |
E | |
| Entrez [Biocaml] | |
| Error [Biocaml_sam_deprecated] | |
| Error [Biocaml_zip] | |
| Error [Biocaml_wig] | |
| Error [Biocaml_track] | |
| Error [Biocaml_table.Row] | |
| Error [Biocaml_psl] | |
| Error [Biocaml_gff] | |
| Error [Biocaml_chr] | |
| Error [Biocaml_bed] | |
| Error [Biocaml_bam] | |
F | |
| Fasta [Biocaml] | |
| Fastq [Biocaml] | |
| Flags [Biocaml_sam_deprecated] | |
| Flags [Biocaml_sam] |
Alignment Types
|
G | |
| Gene [Biocaml_entrez.Make] | |
| Gene_ref [Biocaml_entrez.Make] | |
| GenomeMap [Biocaml] | |
| Gff [Biocaml] | |
H | |
| Header [Biocaml_bam_alt] |
BAM header files contain a plain text SAM header, plus additional
information related to the encoding of the file.
|
| Histogram [Biocaml] | |
I | |
| Illumina [Biocaml_fastq] |
Illumina-specific operations
|
| Interval_tree [Biocaml] | |
J | |
| Jaspar [Biocaml] | |
L | |
| LMap [Biocaml_genomeMap.Make] |
A set of locations with an attached value on each of them
|
| LSet [Biocaml_genomeMap.Make] |
A set of locations (e.g.
|
| Line [Biocaml_internal_utils] | |
| Line [Biocaml] | |
| Lines [Biocaml] | |
| List [Biocaml_internal_utils.Result] | |
M | |
| Make [Biocaml_seq_range] | |
| Make [Biocaml_genomeMap] | |
| Make [Biocaml_entrez] | |
| MakeIO [Biocaml_sam] |
Input/Output
|
| MakeIO [Biocaml_lines] | |
| MakeIO [Biocaml_fastq] |
Input/Output
|
| Math [Biocaml] | |
| Msg [Biocaml] | |
| MzData [Biocaml] | |
O | |
| Object_id [Biocaml_entrez.Make] | |
P | |
| Phred_score [Biocaml] | |
| Pos [Biocaml_internal_utils] | |
| Pos [Biocaml] | |
| Precursor [Biocaml_mzData] | |
| Psl [Biocaml] | |
| Pubmed [Biocaml_entrez.Make] | |
| PubmedSummary [Biocaml_entrez.Make] | |
| Pwm [Biocaml] | |
R | |
| RSet [Biocaml] | |
| Range [Biocaml] | |
| Relation [Biocaml_accu] | |
| Result [Biocaml_internal_utils] | |
| Roman_num [Biocaml] | |
| Row [Biocaml_table] | |
S | |
| Sam [Biocaml] | |
| Sbml [Biocaml] | |
| Selection [Biocaml_genomeMap.Make] |
A collection of non-overlapping regions (e.g.
|
| Seq [Biocaml] | |
| Seq_range [Biocaml] | |
| Sgr [Biocaml] | |
| Solexa_score [Biocaml] | |
| Strand [Biocaml] | |
| Stream [Biocaml_internal_utils] | |
T | |
| Table [Biocaml] | |
| Tags [Biocaml_wig] | |
| Tags [Biocaml_table.Row] | |
| Tags [Biocaml_gff] | |
| Track [Biocaml] | |
| Transform [Biocaml_sam_deprecated] | |
| Transform [Biocaml_zip] | |
| Transform [Biocaml_wig] | |
| Transform [Biocaml_vcf] | |
| Transform [Biocaml] | |
| Transform [Biocaml_track] | |
| Transform [Biocaml_table.Row] | |
| Transform [Biocaml_psl] | |
| Transform [Biocaml_lines] | |
| Transform [Biocaml_gff] | |
| Transform [Biocaml_bed] | |
| Transform [Biocaml_bam] | |
| Tree [Biocaml_msg] |
Message tree for more complex messages.
|
U | |
| Url [Biocaml_internal_utils] |
Operations on URL-style encodings.
|
V | |
| Vcf [Biocaml] | |
W | |
| Wig [Biocaml] | |
Z | |
| Zip [Biocaml] |