David Matten's repositories
glycan_detection
glycan_detection
car-price-scraper
a tool to scrape car prices with details from multiple online car sales sites
cluster_align
a tiny bash script to cluster .fasta files at 99% identity with vsearch --cluster_fast, and align all the centroids with mafft.
cluster_analysis
cluster_analysis
contamination_checker
checks for contamination
copy-excel-paste-markdown
Copy a table in Excel (or other spreadsheet programs) and paste it as a Markdown table
davidmatten
davidmatten
disease_visualizer
A project to visualize disease, pathogens, viruses, bacteria and outbreaks on a maps interface, with selectable filters and options like year, kingdom, transmission method.
fasta_tools
a few tools for dealing with fasta files
fastaTools
a few tools for dealing with fasta files
glycan_positional_plotter
Given a .csv file of positions which are occupied across sequences for multiple sequences, we are able to produce a plot assist with visualizing these positions.
list_of_monitised_open_source_projects
I like open source, but its not always simple to monitise an open source project. This repo is dedicated to collecting examples of how others have successfully done this.
PID_analysis
PID_analysis
plotting_with_jitter
plotting_with_jitter
pyfilesystem_test
testing out creating an in memory file system strictly from within python.
python-novice-gapminder
Introduction to Python for non-programmers using gapminder data
real_time_fact_check
A project to detect truth in real time.
reference_numberer
reference_numberer
sampling_from_fasta
Sample from a fasta file.
seq_counter
Very simple sequence counter. Counts the number of sequences in a fasta file, using biopython and SeqIO
staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
theCoolestWorkshopEver
University of Cape Town workshop, Oct. 2017
whereDoThePeopleGo
A repo to explore birth and death rates around the world and over time. Ideally to create animations showing expanding populations and sinks into ways of death
write_by_numbers
A tool to help write long form pieces. This helps to ensure ideas are introduced before they are used, that order of ideas is maintained and allows for tackling smaller bite size pieces of work. Reducing a cognitive load for task switching, and reducing the time requirements to make contributions. Each node has meta, and sentence data, which allows for building networks - and automatically highlighting missing pieces. Enter a node, set up stream requirements (like software might have) and forget about those. They can be filled in later. Continue writing where you are. Then at compile time, upstream sentences will fall into place. No manual moving of content is (possibly allowed) encouraged.