Ribo-Seq and mRNA features forming (analysis) - Revision history

WikiBot: Automatic synchronization with BioUML

2017-02-13T12:00:22Z

Automatic synchronization with BioUML

WikiBot: Protected "Ribo-Seq and mRNA features forming (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

2015-08-25T05:20:08Z

Protected "Ribo-Seq and mRNA features forming (analysis)": Autogenerated page (‎[edit=sysop] (indefinite))

WikiBot: Automatic synchronization with BioUML

2015-08-25T05:20:06Z

Automatic synchronization with BioUML

New page

;Analysis title
:[[File:Default-analysis-icon.png]] Ribo-Seq and mRNA features forming
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|biouml.plugins.bindingregions.mrnaanalysis.RiboSeqAndMrnaFeaturesForming}}
;Plugin
:[[Biouml.plugins.bindingregions (plugin)|biouml.plugins.bindingregions (Binding-regions related analyses)]]

==== Description ====
Create data matrix with Ribo-Seq and mRNA features and write it as TableDataCollection

==== Parameters: ====

* '''Ribo-Seq data set name''' – Select Ribo-Seq data set
* '''Path to folder with data sets''' – Path to folder with data sets
* '''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
* '''Input track''' – Path to domestic track with Ribo-Seq dataset
* '''Minimal reads number threshold''' – Peaks for which number of reads exeeds this threshold will be analized
* '''Start codon type''' – Start codon type
* '''mRNA and Ribo-Seq features''' – Select mRNA and Ribo-Seq features
* '''Do exclude missing data?''' – Do exclude missing data? (If <nowiki>'</nowiki>no<nowiki>'</nowiki> then possible missing data will be included as NaN-values
* '''Output table path''' – Path to the output table

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

@@ Line 13: / Line 13: @@
 ==== Parameters: ====
-* '''Ribo-Seq data set name''' – Select Ribo-Seq data set
+* '''Data set name''' – Select data set
-* '''Path to folder with data sets''' – Path to folder with data sets
 * '''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
-* '''Input track''' – Path to domestic track with Ribo-Seq dataset
+* '''Two tables for calculation of translation (initiation) efficiency, TE (TIE)''' – Two tables for calculation of translation (initiation) efficiency, TE (TIE)
-* '''Minimal reads number threshold''' – Peaks for which number of reads exeeds this threshold will be analized
+** '''Path to table with mRNA-Seq data''' – Path to table with mRNA-Seq data
 * '''Start codon type''' – Start codon type
 * '''mRNA and Ribo-Seq features''' – Select mRNA and Ribo-Seq features
 * '''Do exclude missing data?''' – Do exclude missing data? (If <nowiki>'</nowiki>no<nowiki>'</nowiki> then possible missing data will be included as NaN-values
 * '''Output table path''' – Path to the output table