R / Bioconductor in the AnVIL Cloud
About
Abstract
Incoming expectations
Learning objectives
1
Prerequisites
1.1
Create a google ‘billing account’
1.2
Create an AnVIL account
1.3
Confirm billing project
2
The AnVIL – workspaces, runtimes, buckets, workflows
2.1
Navigation icons
2.2
Use an existing workspace
2.3
DASHBOARD
2.4
DATA
2.5
NOTEBOOKS
2.6
WORKFLOWS
3
Using an existing workspace
3.1
Orchestrating single cell analysis
3.2
Install and load
R
packages
3.3
Example data as a SingleCellExperiment
3.4
The ‘Quick start’ workflow
3.5
Information about the packages used in this session
4
Working with large data
4.1
Human cell atlas data discovery
4.2
R / Bioconductor
libraries
4.3
Data download and import
4.4
‘DelayedArray’ representation of large on-disk data
4.5
Subseting and in-memory location for data exploration
4.6
Exploration of column (cell) annotations
4.7
Invariant cell annotations
4.8
Donor provenance and organ labels
4.9
Sub-setting data based on cell attributes
4.10
Information about the packages used in this session
5
The AnVIL R / Bioconductor package
5.1
R / Bioconductor
libraries
5.2
The
AnVIL
workspace
5.3
Saving analysis products
5.3.1
An abbreviated work flow
5.3.2
Saving results on the runtime instance
5.3.3
Backing up results to the workspace bucket
5.4
Workspace DATA ‘TABLES’
5.4.1
Metadata discovery and export from the HCA
5.4.2
Accessing TABLES
5.4.3
What do we learn about the samples in this experiment?
5.5
Information about the packages used in this session
6
Formal work flows: Human Cell Atlas ‘Optimus’ pipeline
6.1
The HCA Optimus single cell analysis pipeline
6.2
Running a work flow
6.3
Using data in
R
7
Next steps
7.1
Protected data access (US researchers)
7.2
RStudio
7.3
Other clouds
References
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R / Bioconductor in the AnVIL Cloud
References