Workshop 7: Project Resources.
Emma Rand
All the packages mentiond here already installed on the University network
Protein Structure
Read and process pdb files from the Protein Data Bank
- Package: Bio3d
- Bio3D tutorials
Sequences
Import and analyse fasta files.
- Package: seqinr
- Covers using seqin: Applied statistics for bioinformatics using R by Krijnen
- Huge package which includes workflows Bioconductor
- An example workflow Introduction to Bioconductor for Sequence Data with overview
Image analysis
mage processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors.
- Package: EBImage
- A tutorial Basics of image data and spatial patterns analysis in R
Literature Analysis
Search for open access articles, download those articles in full text if available, convert pdf format to plain text, and extract text chunks for vizualization/analysis
- Package: fulltext
- fulltext vignette
