Difference between revisions of "RPR-Biostrings"
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The biostrings R Package | The biostrings R Package | ||
− | + | <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) | |
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− | Introduction to the biostrings bioconductor package | ||
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− | <div | + | <div style="font-size:118%;"> |
− | + | <b>Abstract:</b><br /> | |
<section begin=abstract /> | <section begin=abstract /> | ||
− | < | + | The <tt>biostrings::</tt> 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. |
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<section end=abstract /> | <section end=abstract /> | ||
+ | </div> | ||
+ | <!-- ============================ --> | ||
+ | <hr> | ||
+ | <table> | ||
+ | <tr> | ||
+ | <td style="padding:10px;"> | ||
+ | <b>Objectives:</b><br /> | ||
+ | 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. | ||
+ | </td> | ||
+ | <td style="padding:10px;"> | ||
+ | <b>Outcomes:</b><br /> | ||
+ | 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. | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | <!-- ============================ --> | ||
+ | <hr> | ||
+ | <b>Deliverables:</b><br /> | ||
+ | <section begin=deliverables /> | ||
+ | <li><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.</li> | ||
+ | <li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li> | ||
+ | <li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li> | ||
+ | <section end=deliverables /> | ||
+ | <!-- ============================ --> | ||
+ | <hr> | ||
+ | <section begin=prerequisites /> | ||
+ | <b>Prerequisites:</b><br /> | ||
+ | This unit builds on material covered in the following prerequisite units:<br /> | ||
+ | *[[RPR-FASTA|RPR-FASTA (FASTA files with R)]] | ||
+ | <section end=prerequisites /> | ||
+ | <!-- ============================ --> | ||
+ | </div> | ||
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− | + | __TOC__ | |
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=== Evaluation === | === Evaluation === | ||
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<b>Evaluation: NA</b><br /> | <b>Evaluation: NA</b><br /> | ||
− | :This unit is not evaluated for course marks. | + | <div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div> |
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− | </div | ||
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== Contents == | == Contents == | ||
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+ | {{ABC-unit|RPR-Biostrings.R}} | ||
== Further reading, links and resources == | == Further reading, links and resources == | ||
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<div class="about"> | <div class="about"> | ||
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:2017-08-05 | :2017-08-05 | ||
<b>Modified:</b><br /> | <b>Modified:</b><br /> | ||
− | : | + | :2020-09-24 |
<b>Version:</b><br /> | <b>Version:</b><br /> | ||
− | :0.1 | + | :1.0.1 |
<b>Version history:</b><br /> | <b>Version history:</b><br /> | ||
+ | *1.1 2020 Maintenance | ||
+ | *1.0 First live version 2017 | ||
*0.1 First stub | *0.1 First stub | ||
</div> | </div> | ||
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{{CC-BY}} | {{CC-BY}} | ||
+ | [[Category:ABC-units]] | ||
+ | {{UNIT}} | ||
+ | {{LIVE}} | ||
</div> | </div> | ||
<!-- [END] --> | <!-- [END] --> |
Latest revision as of 10:42, 24 September 2020
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:
|
Outcomes:
|
Deliverables:
Prerequisites:
This unit builds on material covered in the following prerequisite units:
Evaluation
Evaluation: NA
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.
Further reading, links and resources
- Biostrings Quick Overview ( summary of Biostrings functions (PDF))
About ...
Author:
- Boris Steipe <boris.steipe@utoronto.ca>
Created:
- 2017-08-05
Modified:
- 2020-09-24
Version:
- 1.0.1
Version history:
- 1.1 2020 Maintenance
- 1.0 First live version 2017
- 0.1 First stub
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.