C. Titus Brown (@ctb)
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Top repositories

1

pony-build

A simple continuous integration system, written in Python.
Python
87
star
2

advanced-swc

Intermediate and Advanced Software Carpentry tutorial material
Python
72
star
3

twill-legacy

A simple command-line Web browser, for testing and Web automation.
Python
58
star
4

figleaf

A code coverage recording and analysis tool for Python
Python
33
star
5

theproj

Test project for software carpentry
Python
31
star
6

2013-pycon-awesome-big-data-algorithms

31
star
7

2019-snakemake-ucdavis

Intro to workflows for efficient automated data analysis, using snakemake.
30
star
8

SomePackage

A simple example package for thinking about test packaging.
Python
29
star
9

meep

Meep! A simple messageboard implementation for a class.
Python
23
star
10

titus-blog

My blog.
HTML
16
star
11

khmer-ngram

Simple probabilistic de Bruijn graph representation
Python
13
star
12

edda

JavaScript
13
star
13

2012-paper-diginorm

Paper source, analysis notebook, and data generation/analysis scripts for diginorm paper
Python
9
star
14

2017-ucdavis-igg201b

Jupyter Notebook
9
star
15

willow

Genome visualization on the cheap
Python
9
star
16

blastkit

Python
9
star
17

labibi

Python
8
star
18

2016-mybinder-irkernel

Jupyter Notebook
7
star
19

pygr-draw

Simple drawing code for pygr features
Python
7
star
20

deepchem-book

Code exploration from Deep Learning for the Life Sciences: Applying Deep Learning to Genomics, Microscopy, Drug Discovery, and More
Jupyter Notebook
6
star
21

www-ged.msu.edu

Lab Web site at MSU
JavaScript
6
star
22

2019-snakemake-slurm

A simple snakefile to play with slurm foo
Python
5
star
23

2014-megahit-evaluation

5
star
24

guppy

GED Lab Python scripts / bioinformatics trivia
Python
4
star
25

2017-binder-workshop-notes

4
star
26

zounds

Worker bee software for using BLAST and HMMER in Beowulf-style environments
Python
4
star
27

2017-tara-binning

Standard ML
4
star
28

2013-reproducible-bioinfo

4
star
29

2018-snakemake-cli

Python
4
star
30

2016-mybinder-inflammation

Jupyter Notebook
4
star
31

motility

Prolog
4
star
32

scotch

A simple WSGI recording & playback interface, with a proxy server.
Python
3
star
33

2020-long-read-assembly-decontam

Try 2 of detecting/removing microbial contamination from long-read assemblies.
Python
3
star
34

surely

Python
3
star
35

hmmertree

Exploring distance-matrix-based clustering of HMMER results
Python
3
star
36

2020-jgi-tech-talk

JGI Tech Talk binder repo
Standard ML
3
star
37

sourmash_plugin_commonhash

sourmash plugin to filter hashes/k-mers by presence across many sketches
Python
3
star
38

2021-snakemake-checkpoints-example

3
star
39

cse491-2012-examples

3
star
40

eel-pond

Python
3
star
41

2022-assembly-summary-to-lineages

Convert NCBI assembly_summary files into sourmash taxonomy databases.
Python
3
star
42

2015-docker-building

Shell
3
star
43

ribbity

Python
3
star
44

2015-khmer-sequence-bloom-trees

Python
3
star
45

magsearch

Workflow and config files for searching (very) large public databases with sourmash sketches
Standard ML
3
star
46

lqueue

Simple localhost FIFO queue
Python
2
star
47

2020-stacked-dot-plots

HTML
2
star
48

2015-sbt-demo

Python
2
star
49

paircomp

C++
2
star
50

pygr-examples

Python
2
star
51

paper-reviews

2
star
52

ngs-notebooks

Python
2
star
53

lamprey-est-map

Python
2
star
54

sartre

Python
2
star
55

2017-sourmash-cluster

Jupyter Notebook
2
star
56

2017-moore-ddd-annual-report

2
star
57

sourmash_plugin_template_test1

testing the plugin template!
Python
2
star
58

2019-upr-kmers

A binderized repo on DNA k-mers, for a bio/Big Data class at U Puerto Rico Rio Piedras
Jupyter Notebook
2
star
59

2022-sourmash-sens-spec

Playing around with sens/spec measurements for simulated stuff
Jupyter Notebook
2
star
60

beacon

BEACON course
Python
2
star
61

2021-sourmash-unroll-compare

Python
2
star
62

resume

My CV & resume.
TeX
2
star
63

2024-human-contam

Explore microbial contamination in human whole-genome shotgun data sets, using sourmash
Python
2
star
64

2014-streaming

TeX
1
star
65

www-pygr.org

pygr Web site
Shell
1
star
66

2017-sourmash-lca

Python
1
star
67

2020-ggg298-class9

Python
1
star
68

2018-tamer-transcriptome

Python
1
star
69

qingpeng-cv

TeX
1
star
70

dbg-graph-null

Python scripts to generate random genomes and reads
Python
1
star
71

2018-clustering-bins-example

Jupyter Notebook
1
star
72

swc-git-intermediate-bisect

1
star
73

2015-pycon-talk

HTML
1
star
74

2016-lessons-from-gerry

An article for my father's memorial volume
TeX
1
star
75

sourmash_plugin_load_from_fasta

An experimental plugin to load sketches from a FASTA/FASTQ file with lazy sketching.
Python
1
star
76

2019-tara-binning2

More explorations of Tara ocean data set binning foo
Python
1
star
77

2017-sourmash-binder-demo

Jupyter Notebook
1
star
78

waroo

genome annotation
Python
1
star
79

makeitso

Python
1
star
80

2022-github-classroom-example

github classroom example
1
star
81

2022-sourmash-sqlite

Storing sourmash signatures/sketches in a SQLite database
Python
1
star
82

ctb.github.com

ctb's github site
1
star
83

cse491-webz

Python
1
star
84

2015-davis-t3-day3

Example for #t3davis
Python
1
star
85

test2

1
star
86

bags

Bacterial genomics with pygr
Python
1
star
87

2021-sourmash-datasette

Exploring datasette for exploring microbial taxonomy analyses of metagenomes wit hsourmash
Python
1
star
88

2023-ems-worm-genomes

Jupyter Notebook
1
star
89

2016-phil-openscience

1
star
90

2021-sourmash-jsonrpc

A simple JSON RPC client/server setup for sourmash databases
Python
1
star
91

2020-distance-compare

Python
1
star
92

speet

Python
1
star
93

2022-sourmash-uniqify

Greedy iterative clustering of genomes using sourmash
Python
1
star
94

2021-petabyte-example

Python
1
star
95

herbert

Shell
1
star
96

cse891-fall-2011-test

1
star
97

pony-build-git-test

Test repository for pony-build's git client.
1
star