jlumpe

Computational biologist and bioinformatics software developer.

Sunnyvale, CA

Pinned Repositories

gambit
A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
Language:Python29 1 14
gambit-publication
Snakemake workflow to generate figures and results from GAMBIT paper
Language:Python2 1 00
geodesiclm
Geodesic Levenberg-Marquardt
Language:Fortran43
nbcat
View contents of Jupyter notebooks in the terminal with syntax highlighting.
Language:Python4 2 00
org-json
Export org mode files/elements to JSON.
Language:Emacs Lisp4 2 01
ox-json
JSON export back end for Emacs Org mode
Language:Emacs Lisp83 4 66
pyorg
Python library for working with Emacs org mode.
Language:Python34 3 43
pyorg-flask
Flask app for pyorg package
Language:Python12 3 02
python-emacs
Python interface to GNU Emacs.
Language:Python20 3 12
triarray
Python package for working with pairwise distance/similarity matrices in non-redundant format.
Language:Python4 2 02

jlumpe's Repositories

jlumpe/ox-json
JSON export back end for Emacs Org mode
Language:Emacs Lisp83 4 66
jlumpe/pyorg
Python library for working with Emacs org mode.
Language:Python34 3 43
jlumpe/gambit
A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
Language:Python29 1 14
jlumpe/python-emacs
Python interface to GNU Emacs.
Language:Python20 3 12
jlumpe/pyorg-flask
Flask app for pyorg package
Language:Python12 3 02
jlumpe/triarray
Python package for working with pairwise distance/similarity matrices in non-redundant format.
Language:Python4 2 02
jlumpe/gambit-publication
Snakemake workflow to generate figures and results from GAMBIT paper
Language:Python2 1 00
jlumpe/progress-interface
Generic interface for monitoring task progress in Python.
Language:Python1 2 0
jlumpe/pyskeleton
Skeleton Python project
Language:Python1 1 0
jlumpe/AbstractTrees.jl
Abstract julia interfaces for working with trees
Language:Julia1 0
jlumpe/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell1 0
jlumpe/biopython
Official git repository for Biopython (originally converted from CVS)
Language:Python1 0
jlumpe/entrez-tools
Tools to make working with the Entrez EUtils more bearable.
Language:Python2 0
jlumpe/HexGrids.jl
Julia package for working with hexagonal grids.
Language:Julia1 0
jlumpe/IJulia.jl
Julia kernel for Jupyter
Language:Julia1 0
jlumpe/jlumpe-gambit-lab-nb
Jared Lumpe's digital lab notebook for MIDAS project
Language:Jupyter Notebook
jlumpe/julia
The Julia Language: A fresh approach to technical computing.
Language:Julia1 0
jlumpe/Manifolds.jl
Manifolds.jl aims to provide both a unified interface to define and use manifolds as well as a library of manifolds to use for your projects.
Language:Julia1 0
jlumpe/ManifoldsBase.jl
Basic interface for manifolds in Julia
Language:Julia1 0
jlumpe/midas
Early version of the GAMBIT tool.
Language:Python
jlumpe/miniwdl
Workflow Description Language developer tools & local runner
Language:Python0 0
jlumpe/paperpile-tools
Tools to remove some of the annoyances in Paperpile
Language:Python2 1
jlumpe/pydatatypes
Python package for working with pseudo-statically-typed data.
Language:Python
jlumpe/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
Language:Python0 0
jlumpe/seaborn
Statistical data visualization using matplotlib
Language:Python2 0
jlumpe/Snowflake.jl
Models of snowflake growth in Julia.
Language:Julia1 0
jlumpe/staphb-docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
Language:Dockerfile0 0
jlumpe/SurrealNumbers.jl
Implementation of the surreal numbers in Julia.
Language:Julia2 0
jlumpe/WebIO.jl
A bridge between Julia and the Web.
Language:Julia1 0
jlumpe/wgs-kmers
Ancient ancestor of the GAMBIT tool.
Language:Python3 1