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使用Bioconductor分析基因组科学数据

约翰霍普金斯大学

4（186 个评分） | 10K 名学生已注册

课程 6（共 8 门，基因组数据科学专项课程）

Learn to use tools from the Bioconductor project to perform analysis of genomic data. This is the fifth course in the Genomic Big Data Specialization from Johns Hopkins University.

查看授课大纲

您将学习的技能

Bioinformatics, Bioconductor, Genomics, R Programming

审阅

4（186 个评分）

5 stars
87 ratings
4 stars
52 ratings
3 stars
23 ratings
2 stars
9 ratings
1 star
15 ratings

AB

Apr 12, 2018

Amazing course, motivated me to use bio conductor for descriptive seq studies of DNA.

CZ

Feb 10, 2016

I learned a lot from this class and the instructor is good.

从本节课中

Week One

The class will cover how to install and use Bioconductor software. We will discuss common data structures, including ExpressionSets, SummarizedExperiment and GRanges used across several types of analyses.

What is Bioconductor7:17

Installing Bioconductor3:39

The Bioconductor Website9:55

Useful Online Resources5:08

R Base Types18:11

GRanges - Overview4:41

IRanges - Basic Usage12:11

GenomicRanges - GRanges8:44

GenomicRanges - Basic GRanges Usage8:14

GenomicRanges - seqinfo6:13

AnnotationHub8:22

Usecase: AnnotationHub and GRanges, part 112:55

Usecase: AnnotationHub and GRanges, part 213:45

教学方

Kasper Daniel Hansen, PhD
Assistant Professor, Biostatistics and Genetic Medicine

脚本

In this session we will discuss how to get help online with Bioconductor.

The most useful resource for online help with Bioconductor is the support site or

the support forum.

You can navigate to that by going to the Bioconductor webpage.

And out here to the right under learn, there's a port site.

That gets taken to a standout form.

We can see we have questions here people can answer.

And out here underneath the title of the question,

you can see that each question gets automatically checked.

With a number of text.

This ensures that questions about specific packages

gets forwarded also to the packet's main chain, who may or may not answer.

It takes a little bit of learning to learn

how to efficiently ask a question on a mailing list.

There's a guide for

that if we go back to the bottom of the webpage down on the uses.

You can see there is also a link to the support site, a little confusing.

And here's a little text about the support site.

And there is a link to a posting guide, which I highly recommend that people use.

Key information is that when you ask a question,

you try to always include the output of session info.

Session info is and there's a little r function that

displays the current state of your system which is highly useful.

Another thing that I find when people ask questions

is that they tend to include too little information in their postings.

The way I like to ask questions is,

I like to ask a clean, short question.

And then below the question I copy and paste all the output that I need.

The code that I am using, and all the information.

That may take up a lot of space sometimes.

I've even copied thousands of lines of output into the question, but

that is sometimes necessary for people to help you efficiently.

So I'll encourage everybody to sign up for the support site and

to use it and to eventually graduate to a level

where you can start helping other people with their problems.

An alternative to support site is a stack overflow.

Stack overflow is a website that provides forms for

a lot of computer related questions.

[COUGH] And

they can tack their questions using different programming languages and

environments that we insert for Bioconductor.

[COUGH] We get a little test of whether we are humans.

And here's a tag for Bioconductor.

Once I click on.

[COUGH] And now I have everything that's being tagged with Bioconductor.

This is also useful, this is not a form that I use myself but it's highly used in

computer science and for some programming language, it's incredibly helpful.

Let's now transition to something slightly different which is searching for

help in online documentation.

So our search with documentation from packages that you've installed.

That's very useful.

But sometimes you want to search for a function you've heard about or

you've read about, you don't know which package it's in,

you don't really know what search term you should use and so on, and for

that purpose there are two, I would say, competing online resources.

The first thing is called rdocumentation which gives

you this very nice Search box here where we can search for

specific packages, function names, description, authors and so on.

This searches the rdocumentation across all packages in Cran and

all packages in Bioconductor, and possibly other places.

So let's search for a function here.

Let's look for fund overlaps,

which is a function we will learn to love in this course.

And here's some hits on some help pages.

[COUGH] An alternative to

rdocumentation is another website called rseek.

It does a little bit of the same but it uses a different search interface.

It looks very much like Google.

We have this nice minimalist bar here.

Let's search for findOverlaps.

It also searches across R documentation, but

as you can see here it searches the support site, it searches R bloggers.

And I call them all the resources.

I use both of them occasionally and

I'm still trying to make up my mind which one I like the best.

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