package bistro-bio

You can search for identifiers within the package.

in-package search v0.2.0

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 'a format

val bam : Formats.bam format

val sam : Formats.sam format

val sort : 
  ?on:[ `name | `position ] ->
  Formats.bam Bistro.file ->
  Formats.bam Bistro.file

val indexed_bam_of_sam : 
  Formats.sam Bistro.file ->
  [ `indexed_bam ] Bistro.directory

val indexed_bam_of_bam : 
  Formats.bam Bistro.file ->
  [ `indexed_bam ] Bistro.directory

val indexed_bam_to_bam : 
  [ `indexed_bam ] Bistro.directory ->
  Formats.bam Bistro.file

val bam_of_sam : Formats.sam Bistro.file -> Formats.bam Bistro.file

val sam_of_bam : Formats.bam Bistro.file -> Formats.sam Bistro.file

val view : 
  output:'o format ->
  ?h:bool ->
  ?_H:bool ->
  ?q:int ->
  < file_kind : [ `regular ] ; format : [< `bam | `sam ].. > Bistro.file ->
  'o Bistro.file

val faidx : Formats.fasta Bistro.file -> [ `indexed_fasta ] Bistro.directory

val fasta_of_indexed_fasta : 
  [ `indexed_fasta ] Bistro.directory ->
  Formats.fasta Bistro.file

val flagstat : 
  < Bistro.regular_file_t ; format : [< `bam | `sam ].. > Bistro.file ->
  Bistro.text Bistro.file

val rmdup : 
  ?single_end:bool ->
  [ `indexed_bam ] Bistro.directory ->
  Formats.bam Bistro.file