Daniel C. Jones

hat-trie. An efficient trie implementation.

mk. make remade

proseg. Probabilistic cell segmentation for in situ spatial transcriptomics

coitrees. A very fast interval tree data structure

fastq-tools. Small utilities for working with fastq sequence files.

quip. Compressing next-generation sequencing data with extreme prejudice.

Judo.jl. A Julia document generator

isolator. Rapid and robust analysis of RNA-Seq experiments.

colormake. colorize GNU make output

polee. Analyzing RNA-Seq with approximate likelihood

RecursiveSparseBlocks.jl. julia interface to the librsb sparse matrix library

subsample. Randomly sample lines from massive text files efficiently

Skia.jl. Experimental skia bindings

vanity. scRNA-Seq normalization for the vain

seqbias. An R package to correct for sequence bias in RNA-Seq experiments.

Switch.jl. A C-style switch statement for Julia

fastlog. A faster, reduced-precision logarithm function.

maxspin. Quantifying spatial information in spatial transcriptomics

SpuriousCoexpression.jl. Benchmarking tool for spatial transcriptomics segmentation

Zlib.jl. zlib bindings for Julia

cbgb. computational biology grab-bag: messy one-off scripts for a variety of tasks

PoleeClassifier.jl. Julia

sls. Stochastic L-Systems in Python

Showoff.jl. Nicely format an array of n things for tables and plots

color.jl. Pretty colors for Julia

LazySequences.jl. Lazy sequences.

ragel-julia. A Julia backend for Ragel

isolator-paper. The Isolator Paper

gtf-parse-off. Experiments with parsing gene transfer format

ulam-death-spiral. Exposing the depravity of the natural numbers.

Stepwell.jl. Julia

AnnDatas.jl. Julia compatibility for the anndata python module

prodx. Negative binomial regression for single-cell count data

quip-paper. A paper describing and evaluating the quip compression algorithm.

doozer. Go client driver for doozerd, a consistent, distributed data store

seqsim. A simplistic RNA-Seq simulator.

vim-mk. Vim syntax for mk

GatedLinearNetworks.jl. A gaussian gated linear networks implementation

HATTries.jl. julia hat-trie bindings

julia-minimalist-vim. Alternate vim syntax definitions for Julia

gadfly-static-html. Static HTML documentation for Gadfly

quip-website. A very simple website for quip.

peakolator. World's fastest genomic segmentation algorithm.

peakolator-legacy. Some old code.

dotfiles. Vim Script

countdown. Simple and fast probabilistic nmf for count data

doozerd. A consistent distributed data store.