Difference between revisions of "RPR-Biostrings"
m |
m |
||
| Line 19: | Line 19: | ||
| − | {{ | + | {{DEV}} |
{{Vspace}} | {{Vspace}} | ||
| Line 29: | Line 29: | ||
<section begin=abstract /> | <section begin=abstract /> | ||
<!-- included from "../components/RPR-Biostrings.components.wtxt", section: "abstract" --> | <!-- included from "../components/RPR-Biostrings.components.wtxt", 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. |
<section end=abstract /> | <section end=abstract /> | ||
| Line 40: | Line 40: | ||
<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" --> | <!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" --> | ||
You need to complete the following units before beginning this one: | You need to complete the following units before beginning this one: | ||
| − | *[[RPR-FASTA]] | + | *[[RPR-FASTA|RPR-FASTA (FASTA files with R)]] |
{{Vspace}} | {{Vspace}} | ||
| Line 47: | Line 47: | ||
=== Objectives === | === Objectives === | ||
<!-- included from "../components/RPR-Biostrings.components.wtxt", section: "objectives" --> | <!-- included from "../components/RPR-Biostrings.components.wtxt", section: "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. | ||
{{Vspace}} | {{Vspace}} | ||
| Line 54: | Line 56: | ||
=== Outcomes === | === Outcomes === | ||
<!-- included from "../components/RPR-Biostrings.components.wtxt", section: "outcomes" --> | <!-- included from "../components/RPR-Biostrings.components.wtxt", section: "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. | ||
{{Vspace}} | {{Vspace}} | ||
| Line 84: | Line 89: | ||
== Contents == | == Contents == | ||
<!-- included from "../components/RPR-Biostrings.components.wtxt", section: "contents" --> | <!-- included from "../components/RPR-Biostrings.components.wtxt", section: "contents" --> | ||
| − | . | + | |
| + | {{ABC-unit|RPR-Biostrings.R}} | ||
| + | |||
{{Vspace}} | {{Vspace}} | ||
| Line 155: | Line 162: | ||
:2017-08-05 | :2017-08-05 | ||
<b>Version:</b><br /> | <b>Version:</b><br /> | ||
| − | :0 | + | :1.0 |
<b>Version history:</b><br /> | <b>Version history:</b><br /> | ||
| + | *1.0 First live version 2017 | ||
*0.1 First stub | *0.1 First stub | ||
</div> | </div> | ||
Revision as of 00:55, 22 October 2017
The biostrings R Package
Keywords: Introduction to the biostrings bioconductor package
Contents
This unit is under development. There is some contents here but it is incomplete and/or may change significantly: links may lead to nowhere, the contents is likely going to be rearranged, and objectives, deliverables etc. may be incomplete or missing. Do not work with this material until it is updated to "live" status.
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.
This unit ...
Prerequisites
You need to complete the following units before beginning this one:
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.
Evaluation
Evaluation: NA
- This unit is not evaluated for course marks.
Contents
Task:
- Open RStudio and load the
ABC-unitsR 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.Rand 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))
Notes
Self-evaluation
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
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
