Discover ctb/2019-snakemake-ucdavis Open Source project

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

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A simple continuous integration system, written in Python.

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advanced-swc

Intermediate and Advanced Software Carpentry tutorial material

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twill-legacy

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

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figleaf

A code coverage recording and analysis tool for Python

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theproj

Test project for software carpentry

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2013-pycon-awesome-big-data-algorithms

SomePackage

A simple example package for thinking about test packaging.

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meep

Meep! A simple messageboard implementation for a class.

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titus-blog

My blog.

HTML

khmer-ngram

Simple probabilistic de Bruijn graph representation

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edda

JavaScript

2012-paper-diginorm

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

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2017-ucdavis-igg201b

Jupyter Notebook

willow

Genome visualization on the cheap

Python

blastkit

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labibi

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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

zounds

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

Python

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

2021-sourmash-jsonrpc

A simple JSON RPC client/server setup for sourmash databases

Python

2023-ems-worm-genomes

Jupyter Notebook

2016-phil-openscience

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/2019-snakemake-ucdavis

ctb

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