High-throughput sequencing

1. GEOquery - Bioconductor R package for downloading annotations from GEO database. See this R notebook for usage example.
2. E-utilities - The Entrez Programming Utilities (E-utilities) for querying and retrieving records from NCBI databases such as SRA, PUBMED, GENBANK. reutils is an R package to use E-utilities from within R. See this R notebook for usage example.

Image analysis

1. Imagej - Start here. Offers both GUI-based and script-based interfaces.
2. Pillow - Python library for image analysis

Scientific illustration

1. DNA Features Viewer - Python library for making nice schematics of genes

Sequence alignment

HH-Suite Popular package for sensitive protein sequence searching

Structure

• nglview for visualizing structures in Jupyter Notebook. Can also be integrated into reveal.js presentations.
• PDBx python parser for parsing mmCIF structure files
• APBS & PDB2PQR for biomolecular electrostatics and solvation