Bioinformatics at WVU
1
Introduction
2
Delete Me
3
Getting Started
3.1
Operating Systems
3.1.1
Windows
3.1.2
Mac OS
3.1.3
Linux
3.1.4
HPC
3.2
Text Editor
4
Project Management
4.0.1
Directory Setup
5
Containers
5.1
Example one
5.2
Example two
6
Git and GitHub
7
Software
7.1
Conda
8
Version Tracking
9
Pipelines
10
Documentation
11
Using the HPC
12
Assessing New Tools
13
Writing About Bioinformatics
14
Testing
14.1
Flowchart
15
A Case Study
Set up the project folder and repo
Get the data
15.0.1
Create Conda Environment {-csrna_conda}
Do QC
Quantification
Differential Expression
GO, GSEA, pathway
16
Getting Data
16.1
BaseSpace
16.2
GEO
16.3
TCGA
16.4
SRA
16.5
Your collaborator
16.5.1
ftp
16.5.2
Globus
16.5.3
Google Drive
17
Sharing Data
17.1
SRA
17.2
GEO
17.3
Google Drive
17.4
figshare
17.5
doi
17.6
Me
17.7
Your collaborator
18
Bibliography
Published with bookdown
Doing Bioinformatics at WVU
Chapter 11
Using the HPC