Difference between revisions of "RPR-Biostrings"

From "A B C"
Jump to navigation Jump to search
m
m
Line 1: Line 1:
−
<div id="BIO">
+
<div id="ABC">
−
  <div class="b1">
+
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
The biostrings R Package
 
The biostrings R Package
−
  </div>
+
<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
−
 
+
(Introduction to the biostrings bioconductor package)
−
  {{Vspace}}
+
</div>
−
 
 
−
<div class="keywords">
 
−
<b>Keywords:</b>&nbsp;
 
−
Introduction to the biostrings bioconductor package
 
 
</div>
 
</div>
  
−
{{Vspace}}
+
{{Smallvspace}}
  
  
−
__TOC__
+
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
−
 
+
<div style="font-size:118%;">
−
{{Vspace}}
+
<b>Abstract:</b><br />
−
 
 
−
 
 
−
{{LIVE}}
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
</div>
 
−
<div id="ABC-unit-framework">
 
−
== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
−
<!-- included from "./components/RPR-Biostrings.components.txt", section: "abstract" -->
 
 
The biostrings package in the bioconductor project provides basic support for working with biological sequences. This unit introduces XString objects and some of their methods, and ways to get data into, and out of such objects.
 
The biostrings package in the bioconductor project provides basic support for working with biological sequences. This unit introduces XString objects and some of their methods, and ways to get data into, and out of such objects.
 
<section end=abstract />
 
<section end=abstract />
−
 
+
</div>
−
{{Vspace}}
+
<!-- ============================ -->
−
 
+
<hr>
−
 
+
<table>
−
== This unit ... ==
+
<tr>
−
=== Prerequisites ===
+
<td style="padding:10px;">
−
<!-- included from "./components/RPR-Biostrings.components.txt", section: "prerequisites" -->
+
<b>Objectives:</b><br />
−
<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
 
−
You need to complete the following units before beginning this one:
 
−
*[[RPR-FASTA|RPR-FASTA (FASTA files with R)]]
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
=== Objectives ===
 
−
<!-- included from "./components/RPR-Biostrings.components.txt", section: "objectives" -->
 
 
This unit will ...
 
This unit will ...
 
* ... introduce the Biostrings package;
 
* ... introduce the Biostrings package;
 
* ... teach how to get data into and out of XString, and how to perform simple analyses and transformations.
 
* ... teach how to get data into and out of XString, and how to perform simple analyses and transformations.
−
 
+
</td>
−
{{Vspace}}
+
<td style="padding:10px;">
−
 
+
<b>Outcomes:</b><br />
−
 
 
−
=== Outcomes ===
 
−
<!-- included from "./components/RPR-Biostrings.components.txt", section: "outcomes" -->
 
 
After working through this unit you ...
 
After working through this unit you ...
 
* ... can create DNAString, RNAString and AAString objects;
 
* ... can create DNAString, RNAString and AAString objects;
 
* ... can write code to analyze and transform them;
 
* ... can write code to analyze and transform them;
 
* ... are familiar with XStringSets, and Views and IRanges objects.
 
* ... are familiar with XStringSets, and Views and IRanges objects.
−
 
+
</td>
−
{{Vspace}}
+
</tr>
−
 
+
</table>
−
 
+
<!-- ============================ -->
−
=== Deliverables ===
+
<hr>
−
<!-- included from "./components/RPR-Biostrings.components.txt", section: "deliverables" -->
+
<b>Deliverables:</b><br />
 +
<section begin=deliverables />
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-time_management" -->
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-time_management" -->
 
*<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
 
*<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
Line 72: Line 46:
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
−
 
+
<section end=deliverables />
−
{{Vspace}}
+
<!-- ============================  -->
−
 
+
<hr>
−
 
+
<section begin=prerequisites />
 +
<b>Prerequisites:</b><br />
 +
<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
 +
This unit builds on material covered in the following prerequisite units:
 +
*[[RPR-FASTA|RPR-FASTA (FASTA files with R)]]
 +
<section end=prerequisites />
 +
<!-- ============================  -->
 
</div>
 
</div>
−
<div id="BIO">
 
−
== Contents ==
 
−
<!-- included from "./components/RPR-Biostrings.components.txt", section: "contents" -->
 
  
−
{{ABC-unit|RPR-Biostrings.R}}
+
{{Smallvspace}}
  
  
−
{{Vspace}}
 
  
 +
{{Smallvspace}}
  
−
== Further reading, links and resources ==
 
−
 
−
*{{PDFlink|[https://www.bioconductor.org/packages/release/bioc/vignettes/Biostrings/inst/doc/BiostringsQuickOverview.pdf  Biostrings Quick Overview]| summary of Biostrings functions (PDF)}}
 
  
 +
__TOC__
  
 
{{Vspace}}
 
{{Vspace}}
  
  
−
== Notes ==
+
== Contents ==
−
<!-- included from "./components/RPR-Biostrings.components.txt", section: "notes" -->
+
<!-- included from "./components/RPR-Biostrings.components.txt", section: "contents" -->
−
<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
 
−
<references />
 
−
 
 
−
{{Vspace}}
 
  
 +
{{ABC-unit|RPR-Biostrings.R}}
  
−
</div>
 
−
<div id="ABC-unit-framework">
 
 
== Self-evaluation ==
 
== Self-evaluation ==
−
<!-- included from "./components/RPR-Biostrings.components.txt", section: "self-evaluation" -->
 
 
<!--
 
<!--
 
=== Question 1===
 
=== Question 1===
Line 123: Line 92:
  
 
-->
 
-->
 +
== Notes ==
 +
<!-- included from "./components/RPR-Biostrings.components.txt", section: "notes" -->
 +
<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
 +
<references />
 +
== Further reading, links and resources ==
  
−
{{Vspace}}
+
*{{PDFlink|[https://www.bioconductor.org/packages/release/bioc/vignettes/Biostrings/inst/doc/BiostringsQuickOverview.pdf  Biostrings Quick Overview]| summary of Biostrings functions (PDF)}}
−
 
 
  
  

Revision as of 19:32, 26 January 2018

The biostrings R Package

(Introduction to the biostrings bioconductor package)


 


Abstract:

The biostrings package in the bioconductor project provides basic support for working with biological sequences. This unit introduces XString objects and some of their methods, and ways to get data into, and out of such objects.

Objectives:
This unit will ...

  • ... introduce the Biostrings package;
  • ... teach how to get data into and out of XString, and how to perform simple analyses and transformations.

Outcomes:
After working through this unit you ...

  • ... can create DNAString, RNAString and AAString objects;
  • ... can write code to analyze and transform them;
  • ... are familiar with XStringSets, and Views and IRanges objects.

Deliverables:

  • Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
  • Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
  • Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

Prerequisites:
This unit builds on material covered in the following prerequisite units:


 



 



 


Contents

Task:

 
  • Open RStudio and load the ABC-units R project. If you have loaded it before, choose File → Recent projects → ABC-Units. If you have not loaded it before, follow the instructions in the RPR-Introduction unit.
  • Choose Tools → Version Control → Pull Branches to fetch the most recent version of the project from its GitHub repository with all changes and bug fixes included.
  • Type init() if requested.
  • Open the file RPR-Biostrings.R and follow the instructions.


 

Note: take care that you understand all of the code in the script. Evaluation in this course is cumulative and you may be asked to explain any part of code.


 

Self-evaluation

Notes

Further reading, links and resources


 



 

If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.


 

About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-08-05

Version:

1.0

Version history:

  • 1.0 First live version 2017
  • 0.1 First stub

CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=RPR-Biostrings&oldid=10877"