WikiBot: Automatic synchronization with BioUML

2020-12-09T11:14:38Z

Automatic synchronization with BioUML

WikiBot: Protected "GTRD analysis": Autogenerated page (‎[edit=sysop] (indefinite))

2019-03-12T09:32:19Z

Protected "GTRD analysis": Autogenerated page (‎[edit=sysop] (indefinite))

WikiBot: Automatic synchronization with BioUML

2019-03-12T09:32:18Z

Automatic synchronization with BioUML

New page

;Analysis title
:[[File:Default-analysis-icon.png]] GTRD analysis
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|biouml.plugins.bindingregions.analysis.GtrdAnalysis}}
;Plugin
:[[Biouml.plugins.bindingregions (plugin)|biouml.plugins.bindingregions (Binding-regions related analyses)]]

==== Description ====
Analysis of GTRD peaks

==== Parameters: ====

* '''Option''' – Select option (the concrete session of given analysis).
* '''Parameters for OPTION_01''' – Please, determine parameters for OPTION_01
** '''Sequences collection''' – Select a source of nucleotide sequences
*** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
*** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
** '''Species''' – Select a taxonomical species
** '''Path to folder with tracks''' – Path to folder with (ChIP-seq) tracks
** '''Track size threshold''' – Track size threshold
** '''Path to input table''' – Path to input table
** '''Name of column for chromosome names''' – Select name of the table column for chromosome names
** '''Name of column for TSS positions''' – Select name of the table column for TSS positions
** '''Name of <nowiki>{'</nowiki>+<nowiki>'</nowiki>, <nowiki>'</nowiki>-<nowiki>'}</nowiki>-column for TSS strands''' – Select name of the table column for TSS strands
** '''Promoter regions''' – Promoter regions
* '''Parameters for OPTION_2''' – Please, determine parameters for OPTION_02
** '''Path to folder with tracks''' – Path to folder with (ChIP-seq) tracks
** '''Path to folder with files''' – Path to folder with files that contain coverage matrices
* '''Parameters for OPTION_03''' – Please, determine parameters for OPTION_03
** '''Species''' – Select a taxonomical species
** '''Path to folder with tracks''' – Path to folder with (ChIP-seq) tracks
* '''Parameters for OPTION_04''' – Please, determine parameters for OPTION_04
** '''Path to folder with tracks''' – Path to folder with (ChIP-seq) tracks
** '''Tracks names''' – Select tracks names
** '''Minimal length of site''' – Minimal length of site (or binding region)
** '''Maximal length of site''' – Maximal length of site (or binding region)
* '''Parameters for OPTION_05''' – Please, determine parameters for OPTION_05
** '''Species''' – Select a taxonomical species
** '''Path to folder with folders''' – Path to folder with folders (that contain (ChIP-seq) tracks)
** '''Folders names''' – Select folders names
** '''Minimal length of site''' – Minimal length of site (or binding region)
** '''Maximal length of site''' – Maximal length of site (or binding region)
* '''Parameters for OPTION_06''' – Please, determine parameters for OPTION_06
** '''Species''' – Select a taxonomical species
** '''Path to folder with folders''' – Path to folder with folders (that contain (ChIP-seq) tracks)
** '''Folders names''' – Select folders names
** '''Path to folder with matrices''' – Path to folder with frequency matrices
* '''Parameters for OPTION_07''' – Please, determine parameters for OPTION_07
** '''Sequences collection''' – Select a source of nucleotide sequences
*** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
*** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
** '''Path to input table''' – Path to input table
** '''Path to folder with matrices''' – Path to folder with frequency matrices
** '''Site model type''' – Select site model type
** '''Path to folder with tables''' – Path to folder with tables
** '''Do remove orphans''' – Do remove orphans
** '''Do extract random regions''' – Do extract random regions
** '''Minimal number of regions''' – Minimal number of regions
* '''Parameters for OPTION_08''' – Please, determine parameters for OPTION_08
** '''Sequences collection''' – Select a source of nucleotide sequences
*** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
*** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
** '''Path to input table''' – Path to input table
** '''Path to folder with matrices''' – Path to folder with frequency matrices
* '''Parameters for OPTION_09''' – Please, determine parameters for OPTION_09
** '''Sequences collection''' – Select a source of nucleotide sequences
*** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
*** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
** '''Path to input table''' – Path to input table
** '''Path to folder with matrices''' – Path to folder with frequency matrices
** '''Path to folder with tables''' – Path to folder with tables
** '''Do remove orphans''' – Do remove orphans
** '''Minimal number of regions''' – Minimal number of regions
* '''Path to output folder''' – Path to output folder

[[Category:Analyses]]
[[Category:Binding regions (analyses group)]]
[[Category:ISB analyses]]
[[Category:Autogenerated pages]]

@@ Line 25: / Line 25: @@
 ** '''Name of column for TSS positions''' – Select name of the table column for TSS positions
 ** '''Name of <nowiki>{'</nowiki>+<nowiki>'</nowiki>, <nowiki>'</nowiki>-<nowiki>'}</nowiki>-column for TSS strands''' – Select name of the table column for TSS strands
 * '''Parameters for OPTION_2''' – Please, determine parameters for OPTION_02
 ** '''Path to folder with tracks''' – Path to folder with (ChIP-seq) tracks

GTRD analysis - Revision history

WikiBot: Automatic synchronization with BioUML

WikiBot: Protected "GTRD analysis": Autogenerated page (‎[edit=sysop] (indefinite))

WikiBot: Automatic synchronization with BioUML