package bistro-bio
Bistro workflows for computational biology
Install
Dune Dependency
Authors
Maintainers
Sources
bistro-0.6.0.tbz
sha256=146177faaaa9117a8e2bf0fd60cb658662c0aa992f35beb246e6fd0766050e66
sha512=553fe0c20f236316449b077a47e6e12626d193ba1916e9da233e5526dd39090e8677277e1c79baace3bdc940cb009f25431730a8efc00ae4ed9cc42a0add9609
doc/bistro-bio.examples/Bistro_bio_examples/Chen2008/Dnaseq/index.html
Module Chen2008.DnaseqSource
Source
val mapped_reads :
[ `ES_WT_ChIP_Essrb_Chen2008
| `ES_WT_ChIP_Nanog_Chen2008
| `ES_WT_ChIP_Pou5f1_Chen2008
| `ES_WT_ChIP_Sox2_Chen2008 ] ->
Bistro_bio.Formats.sam Bistro.fileSource
val mapped_reads_indexed_bam :
[ `ES_WT_ChIP_Essrb_Chen2008
| `ES_WT_ChIP_Nanog_Chen2008
| `ES_WT_ChIP_Pou5f1_Chen2008
| `ES_WT_ChIP_Sox2_Chen2008 ] ->
[ `indexed_bam ] Bistro.directorySource
val mapped_reads_bam :
[ `ES_WT_ChIP_Essrb_Chen2008
| `ES_WT_ChIP_Nanog_Chen2008
| `ES_WT_ChIP_Pou5f1_Chen2008
| `ES_WT_ChIP_Sox2_Chen2008 ] ->
Bistro_bio.Formats.bam Bistro.fileSource
val mapped_reads_nodup :
[ `ES_WT_ChIP_Essrb_Chen2008
| `ES_WT_ChIP_Nanog_Chen2008
| `ES_WT_ChIP_Pou5f1_Chen2008
| `ES_WT_ChIP_Sox2_Chen2008 ] ->
Bistro_bio.Formats.bam Bistro.fileSource
val mapped_reads_nodup_indexed :
[ `ES_WT_ChIP_Essrb_Chen2008
| `ES_WT_ChIP_Nanog_Chen2008
| `ES_WT_ChIP_Pou5f1_Chen2008
| `ES_WT_ChIP_Sox2_Chen2008 ] ->
[ `indexed_bam ] Bistro.directorySource
val coverage :
[ `ES_WT_ChIP_Essrb_Chen2008
| `ES_WT_ChIP_Nanog_Chen2008
| `ES_WT_ChIP_Pou5f1_Chen2008
| `ES_WT_ChIP_Sox2_Chen2008 ] ->
Bistro_bio.Ucsc_gb.bigWig Bistro.fileSource
val counts :
no_dups:bool ->
feature_type:string ->
attribute_type:string ->
gff:Bistro_bio.Formats.gff Bistro.file ->
[ `ES_WT_ChIP_Essrb_Chen2008
| `ES_WT_ChIP_Nanog_Chen2008
| `ES_WT_ChIP_Pou5f1_Chen2008
| `ES_WT_ChIP_Sox2_Chen2008 ] ->
[ `featureCounts ] Bistro.directorySource
val fastq_screen :
possible_contaminants:(string * Bistro_bio.Formats.fasta Bistro.file) list ->
[ `ES_WT_ChIP_Essrb_Chen2008
| `ES_WT_ChIP_Nanog_Chen2008
| `ES_WT_ChIP_Pou5f1_Chen2008
| `ES_WT_ChIP_Sox2_Chen2008 ] ->
Bistro.html Bistro.fileSource
val bamstats :
[ `ES_WT_ChIP_Essrb_Chen2008
| `ES_WT_ChIP_Nanog_Chen2008
| `ES_WT_ChIP_Pou5f1_Chen2008
| `ES_WT_ChIP_Sox2_Chen2008 ] ->
Bistro.text Bistro.fileSource
val bamstats_alt :
[ `ES_WT_ChIP_Essrb_Chen2008
| `ES_WT_ChIP_Nanog_Chen2008
| `ES_WT_ChIP_Pou5f1_Chen2008
| `ES_WT_ChIP_Sox2_Chen2008 ] ->
Biocaml_ez.Bamstats.t Bistro.workflowSource
val chrstats :
[ `ES_WT_ChIP_Essrb_Chen2008
| `ES_WT_ChIP_Nanog_Chen2008
| `ES_WT_ChIP_Pou5f1_Chen2008
| `ES_WT_ChIP_Sox2_Chen2008 ] ->
Bistro.text Bistro.file