Data_on_AnVIL/01-intro.Rmd at main · fhdsl/Data_on_AnVIL · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47

```{r, include = FALSE}
ottrpal::set_knitr_image_path()
```

# Introduction

This book contains a collection of vignettes that guide users through different ways to access data on the AnVIL platform.

## Motivation

One of the most common questions people have when using the AnVIL platform is "how do I get the data?" We created this book to provide step-by-step examples for users follow so that they can feel confident finding or moving data onto AnVIL. Each vignette is quick (designed to take ~15 minutes) and will incur minimal costs.

Navigate to the menu on the left to get started!

## Target Audience

The course is intended for new and experienced users of the AnVIL platform. In order to follow the vignettes, **you must have an AnVIL account that is connected to a billing project.** Each vignette will incur only minimal costs.

If you don't have an AnVIL account yet, instructions on getting one can be found at the [AnVIL Portal](https://anvilproject.org/learn/get-started).

::: {.notice}
These vignettes are built around common tasks that an individual user might do. If you are bringing a large amount of data to AnVIL through a consortium, you might find [documentation for Data Submitters](https://anvilproject.org/learn/submit-data) more helpful.
:::

## Curriculum

These vignettes cover the following topics:

**Bringing your own data to AnVIL**
Do you have data stored elsewhere that you need to add to an AnVIL workspace? These vignettes can help you get started.

* Uploading data from your local computer
* Uploading data from the cloud
* Uploading data from a high performance computing cluster

**Getting data from external data repositories**
Are you working with data that you need to retrieve from a non-AnVIL data repository? These vignettes provide details on how to bring that data into an AnVIL workspace.

* Importing data from SRA
* Importing data from dbGaP

**Finding data stored on AnVIL**
Do you want to access a dataset that's been stored on AnVIL? These vignettes cover how to find and retrieve both open and controlled access datasets in the AnVIL data repository.

* Accessing open access data stored on AnVIL
* Accessing controlled access data stored on AnVIL using DUOS