package bistro-bio

You can search for identifiers within the package.

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 sequence_type = [

| `DNA
| `AA
| `BIN
| `MORPH
| `CODON of int
| `NT2AA

]

type dna_model = [

| `JC69
| `F81
| `K80
| `HKY85
| `TN93
| `TNe
| `K81
| `K81u
| `TPM2
| `TPM2u
| `TPM3
| `TPM3u
| `TIM
| `TIMe
| `TIM2
| `TIM2e
| `TIM3
| `TIM3e
| `TVM
| `TVMe
| `SYM
| `GTR

]

type protein_model = [

| `BLOSUM62
| `cpREV
| `Dayhoff
| `DCMut
| `FLU
| `HIVb
| `HIVw
| `JTT
| `JTTDCMut
| `LG
| `mtART
| `mtMAM
| `mtREV
| `mtZOA
| `mtMet
| `mtVer
| `mtInv
| `Poisson
| `PMB
| `rtREV
| `VT
| `WAG

]

type protein_mixture_model = [

| `C10
| `C20
| `C30
| `C40
| `C50
| `C60
| `EX2
| `EX3
| `EHO
| `UL2
| `UL3
| `EX_EHO
| `LG4M
| `LG4X
| `CF4

]

type codon_model = [

| `MG
| `MGK
| `MG1KTS
| `MG1KTV
| `MG2K
| `GY
| `GY1KTS
| `GY1KTV
| `GY2K
| `ECMK07
| `ECMrest
| `ECMS05

]

type binary_model = [

| `JC2
| `GTR2

]

type freq_type = [

| `F
| `FO
| `FQ
| `F1x4
| `F3x4

]

type rate_type = [

| `I
| `G of int option
| `I_G
| `R of int option
| `I_R

]

type model_spec

val model_spec : 
  ?freq_type:freq_type ->
  ?rate_type:rate_type ->
  [ dna_model
  | protein_model
  | protein_mixture_model
  | codon_model
  | binary_model ] ->
  model_spec

val iqtree : 
  ?t:[ `BIONJ | `RANDOM | `Tree of Formats.newick Bistro.file ] ->
  ?te:Formats.newick Bistro.file ->
  ?o:string ->
  ?nt:int ->
  ?seed:int ->
  ?n:int ->
  ?m:model_spec ->
  ?z:Formats.newick Bistro.file ->
  ?st:sequence_type ->
  ?spp:Formats.nexus Bistro.file ->
  ?keep_ident:bool ->
  [ `phylip of Formats.phylip Bistro.file
  | `fasta of Formats.fasta Bistro.file ] ->
  [ `iqtree ] Bistro.directory

val treefile : [ `iqtree ] Bistro.directory -> Formats.newick Bistro.file

val report : [ `iqtree ] Bistro.directory -> Bistro.text Bistro.file