package bistro-bio

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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

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Library
Module
Module type
Parameter
Class
Class type

http://subread.sourceforge.net/

class type count_table = object ... end

val featureCounts : 
  ?feature_type:string ->
  ?attribute_type:string ->
  ?strandness:[ `Unstranded | `Stranded | `Reversely_stranded ] ->
  ?chrAliases:Bistro.csv Bistro.file ->
  ?requireBothEndsMapped:bool ->
  ?countChimericFragments:bool ->
  ?minFragLength:int ->
  ?maxFragLength:int ->
  ?useMetaFeatures:bool ->
  ?allowMultiOverlap:bool ->
  ?fraction:float ->
  ?q:int ->
  ?nthreads:int ->
  Formats.gff Bistro.file ->
  < format : [< `bam | `sam ].. > Bistro.file ->
  [ `featureCounts ] Bistro.directory

val featureCounts_tsv : 
  [ `featureCounts ] Bistro.directory ->
  count_table Bistro.file

val featureCounts_htseq_tsv : 
  [ `featureCounts ] Bistro.directory ->
  Htseq.count_tsv Bistro.file

val featureCounts_summary : 
  [ `featureCounts ] Bistro.directory ->
  Bistro.text Bistro.file