Discover ctb/zounds Open Source project by C. Titus Brown (@ctb)

Stars
4
Rank 3,304,323 (Top 66 %)
Language
Python
Created over 14 years ago
Updated over 14 years ago

ctb

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Worker bee software for using BLAST and HMMER in Beowulf-style environments

pony-build

A simple continuous integration system, written in Python.

Python

advanced-swc

Intermediate and Advanced Software Carpentry tutorial material

Python

twill-legacy

A simple command-line Web browser, for testing and Web automation.

Python

figleaf

A code coverage recording and analysis tool for Python

Python

theproj

Test project for software carpentry

Python

2013-pycon-awesome-big-data-algorithms

2019-snakemake-ucdavis

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

SomePackage

A simple example package for thinking about test packaging.

Python

meep

Meep! A simple messageboard implementation for a class.

Python

titus-blog

My blog.

HTML

khmer-ngram

Simple probabilistic de Bruijn graph representation

Python

edda

JavaScript

2012-paper-diginorm

Paper source, analysis notebook, and data generation/analysis scripts for diginorm paper

Python

2017-ucdavis-igg201b

Jupyter Notebook

willow

Genome visualization on the cheap

Python

blastkit

Python

labibi

Python

2016-mybinder-irkernel

Jupyter Notebook

pygr-draw

Simple drawing code for pygr features

Python

deepchem-book

Code exploration from Deep Learning for the Life Sciences: Applying Deep Learning to Genomics, Microscopy, Drug Discovery, and More

Jupyter Notebook

www-ged.msu.edu

Lab Web site at MSU

JavaScript

2019-snakemake-slurm

A simple snakefile to play with slurm foo

Python

2014-megahit-evaluation

guppy

GED Lab Python scripts / bioinformatics trivia

Python

2017-binder-workshop-notes

2017-tara-binning

Standard ML

2013-reproducible-bioinfo

2018-snakemake-cli

Python

2016-mybinder-inflammation

Jupyter Notebook

motility

Prolog

scotch

A simple WSGI recording & playback interface, with a proxy server.

Python

2020-long-read-assembly-decontam

Try 2 of detecting/removing microbial contamination from long-read assemblies.

Python

surely

Python

hmmertree

Exploring distance-matrix-based clustering of HMMER results

Python

2020-jgi-tech-talk

JGI Tech Talk binder repo

Standard ML

sourmash_plugin_commonhash

sourmash plugin to filter hashes/k-mers by presence across many sketches

Python

2021-snakemake-checkpoints-example

cse491-2012-examples

eel-pond

Python

2022-assembly-summary-to-lineages

Convert NCBI assembly_summary files into sourmash taxonomy databases.

Python

2015-docker-building

Shell

ribbity

Python

2015-khmer-sequence-bloom-trees

Python

magsearch

Workflow and config files for searching (very) large public databases with sourmash sketches

Standard ML

lqueue

Simple localhost FIFO queue

Python

2020-stacked-dot-plots

2015-sbt-demo

paircomp

pygr-examples

paper-reviews

ngs-notebooks

Python

lamprey-est-map

Python

sartre

Python

2017-sourmash-cluster

Jupyter Notebook

2017-moore-ddd-annual-report

sourmash_plugin_template_test1

testing the plugin template!

Python

2019-upr-kmers

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

Jupyter Notebook

2022-sourmash-sens-spec

Playing around with sens/spec measurements for simulated stuff

Jupyter Notebook

beacon

BEACON course

Python

2021-sourmash-unroll-compare

Python

resume

My CV & resume.

TeX

2024-human-contam

Explore microbial contamination in human whole-genome shotgun data sets, using sourmash

2014-streaming

www-pygr.org

2017-sourmash-lca

2020-ggg298-class9

2018-tamer-transcriptome

Python

qingpeng-cv

TeX

dbg-graph-null

Python scripts to generate random genomes and reads

Python

2018-clustering-bins-example

Jupyter Notebook

swc-git-intermediate-bisect

2015-pycon-talk

HTML

2016-lessons-from-gerry

An article for my father's memorial volume

TeX

sourmash_plugin_load_from_fasta

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

Python

2019-tara-binning2

More explorations of Tara ocean data set binning foo

Python

2017-sourmash-binder-demo

waroo

makeitso

2022-github-classroom-example

github classroom example

2022-sourmash-sqlite

Storing sourmash signatures/sketches in a SQLite database

ctb.github.com

cse491-webz

2015-davis-t3-day3

test2

bags

Bacterial genomics with pygr

Python

2021-sourmash-datasette

Exploring datasette for exploring microbial taxonomy analyses of metagenomes wit hsourmash

Python

2023-ems-worm-genomes

Jupyter Notebook

2016-phil-openscience

2021-sourmash-jsonrpc

A simple JSON RPC client/server setup for sourmash databases

Python

2020-distance-compare

Python

speet

Python

2022-sourmash-uniqify

Greedy iterative clustering of genomes using sourmash

Python

2021-petabyte-example

Python

herbert

Shell

cse891-fall-2011-test

pony-build-git-test

Test repository for pony-build's git client.

ctb/zounds

ctb

Reviews

Repository Details

More Repositories