paulstothard/helpful_commands

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Created about 4 years ago
Updated about 1 month ago

paulstothard/helpful_commands

paulstothard

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Command-line tools, commands, and code snippets for performing routine data processing and bioinformatics tasks.

sequence_manipulation_suite

A collection of simple JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. The Sequence Manipulation Suite is commonly used by molecular biologists, for teaching purposes, and for program and algorithm testing.

cgview

CGView is a Java package for generating high-quality, zoomable maps of circular genomes.

cgview_comparison_tool

The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.

helpful_links

Links to resources related to bioinformatics and data analysis.

ncbi_search

This script uses NCBI's Entrez Programming Utilities to perform searches of NCBI databases. This script can return either the complete database records, or the IDs of the records.

fast-pptx

Generate Markdown and PowerPoint slides from a folder of images, code snippets, and other files.

document-builder

Produces nicely formatted PDF and HTML documents from Markdown source files.

dotfiles

Configuration files for bash, tmux, and vim, and a Brewfile for installing software on macOS.

genotype_conversion_file_builder

A pipeline for determining the genomic location and transformation rules for the variants described in Illumina or Affymetrix genotype panel manifest files.

sort_markdown_by_headings

Sorts a Markdown file based on headings.