package bistro-bio

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in-package search v0.2.0

package bistro-bio

bistro-bio
- Bistro_bio
  - Alignment_stats
  - Bed
  - Bedtools
    
    Cmd
  - Bowtie
  - Bowtie2
  - Busco
  - ChIPQC
  - Cisa
  - Cisbp
  - Comparative_genomics
  - DESeq2
    
    table
  - Deeptools
    
    compressed_numpy_array
    
    deeptools_matrix
  - Dnaseq_with_reference_genome
    
    Make
    
    S
    
    Sample
  - Ensembl
  - FastQC
  - Fasta
  - Fastq
  - Fastq_sample
    
    Data
    
    Make
    
    Data
  - Fastq_screen
  - Formats
    
    bam
    
    bed3
    
    bed4
    
    bed5
    
    bed6
    
    fasta
    
    fastq
    
    gff
    
    gff2
    
    gff3
    
    newick
    
    nexus
    
    nhx
    
    phred64_fastq
    
    phylip
    
    sam
    
    sanger_fastq
    
    solexa_fastq
    
    sra
  - Gff
  - Hisat2
  - Htseq
    
    count_tsv
  - Idba
  - Idr
  - Iqtree
  - Jaspar
  - Kallisto
    
    abundance_table
    
    index
  - Macs
    
    narrow_peaks
    
    peak_summits
    
    peaks_xls
  - Macs2
    
    broad_peaks
    
    narrow_peaks
    
    peak_summits
    
    peaks_xls
  - Meme_suite
  - Ncbi_genome
  - Phyml
  - Picardtools
  - Prokka
  - Quast
  - Raxml
  - SE_or_PE
  - Samtools
  - Spades
  - Sra_toolkit
  - Srst2
  - Star
  - Subread
    
    count_table
  - Tophat
  - Trinity
  - Ucsc_gb
    
    Lift_over
    
    chain_file
    
    bedGraph
    
    bigBed
    
    bigWig
    
    chrom_sizes
    
    twobit
    
    wig
bistro-bio.examples
- Bistro_bio_examples
  - Chen2008
    
    Dnaseq
    
    FQS
    
    Sample
  - Zhou2011

Legend:
Library
Module
Module type
Parameter
Class
Class type

type t =

| Fq of Formats.fastq Bistro.file SE_or_PE.t
| Fq_gz of Formats.fastq Bistro.gz Bistro.file SE_or_PE.t

val is_single_end : t -> bool

val plain_se : Formats.fastq Bistro.file -> t

val plain_pe : Formats.fastq Bistro.file -> Formats.fastq Bistro.file -> t

val compressed_se : Formats.fastq Bistro.gz Bistro.file -> t

val compressed_pe : 
  Formats.fastq Bistro.gz Bistro.file ->
  Formats.fastq Bistro.gz Bistro.file ->
  t

val dep : t -> Bistro.Shell_dsl.template SE_or_PE.t

val explode : 
  t list ->
  (Formats.fastq Bistro.file list
   * Formats.fastq Bistro.file list
   * Formats.fastq Bistro.file list)
  * (Formats.fastq Bistro.gz Bistro.file list
     * Formats.fastq Bistro.gz Bistro.file list
     * Formats.fastq Bistro.gz Bistro.file list)

type source =

| Fastq_url of string SE_or_PE.t
| Fastq_gz_url of string SE_or_PE.t
| SRA_dataset of {
1. srr_id : string;
2. library_type : [ `single_end | `paired_end ];
}

val fastq_of_source : source -> Formats.fastq Bistro.file SE_or_PE.t

val fastq_gz_of_source : 
  source ->
  Formats.fastq Bistro.gz Bistro.file SE_or_PE.t

val of_source : source -> t

module type Data = sig ... end

module Make (Data : Data) : sig ... end