dcjones

Staff Scientist at Fred Hutchinson Cancer Center, focusing on spatial transcriptomics, while dabbling in data structures and scientific graphics.

Fred Hutchinson Cancer CenterSeattle, WA, USA

Pinned Repositories

coitrees
A very fast interval tree data structure
Language:Rust125 7 1010
fastq-tools
Small utilities for working with fastq sequence files.
Language:C123 11 2540
hat-trie
An efficient trie implementation.
Language:C255 12 2346
Judo.jl
A Julia document generator
Language:Julia57 8 1513
maxspin
Quantifying spatial information in spatial transcriptomics
Language:Jupyter Notebook5 2 10
mk
make remade
Language:Go178 6 624
polee
Analyzing RNA-Seq with approximate likelihood
Language:Julia26 3 01
proseg
Probabilistic cell segmentation for in situ spatial transcriptomics
Language:Rust126 6 5311
quip
Compressing next-generation sequencing data with extreme prejudice.
Language:C83 4 3012
Gadfly.jl
Crafty statistical graphics for Julia.
Language:Julia1.9k 52 1.1k251

dcjones's Repositories

dcjones/hat-trie
An efficient trie implementation.
Language:C255 12 2346
dcjones/mk
make remade
Language:Go178 6 624
dcjones/proseg
Probabilistic cell segmentation for in situ spatial transcriptomics
Language:Rust126 6 5311
dcjones/coitrees
A very fast interval tree data structure
Language:Rust125 7 1010
dcjones/fastq-tools
Small utilities for working with fastq sequence files.
Language:C123 11 2540
dcjones/quip
Compressing next-generation sequencing data with extreme prejudice.
Language:C83 4 3012
dcjones/polee
Analyzing RNA-Seq with approximate likelihood
Language:Julia26 3 01
dcjones/vanity
scRNA-Seq normalization for the vain
Language:Python8 2 0
dcjones/maxspin
Quantifying spatial information in spatial transcriptomics
Language:Jupyter Notebook5 2 10
dcjones/PoleeClassifier.jl
Language:Julia5 2 1
dcjones/SpuriousCoexpression.jl
Benchmarking tool for spatial transcriptomics segmentation
Language:Julia3 1 0
dcjones/AnnDatas.jl
Julia compatibility for the anndata python module
Language:Julia2 2 0
dcjones/GatedLinearNetworks.jl
A gaussian gated linear networks implementation
Language:Julia1 3 0
dcjones/prodx
Negative binomial regression for single-cell count data
Language:Python1
dcjones/Stepwell.jl
Language:Julia1 1 0
dcjones/Baysor
Bayesian Segmentation of Spatial Transcriptomics Data
Language:Julia1 0
dcjones/BioAlignments.jl
Sequence alignment tools
Language:Julia3 0
dcjones/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell2 0
dcjones/Cronenberg.jl
Simulating spatial expression data
Language:Julia2 0
dcjones/DecisionTree.jl
Julia implementation of Decision Tree (CART) and Random Forest algorithms
Language:Julia1 0
dcjones/ecosystem-packages
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Language:Python1 0
dcjones/gccontent-benchmark
Benchmarking different languages for a simple bioinformatics task (Counting the GC fraction of DNA in a FASTA file)
Language:Rust2 0
dcjones/GCNN.jl
Group CNNs
Language:Julia2 0
dcjones/IntervalTrees.jl
A data structure for efficient manipulation of sets of intervals
Language:Julia3 0
dcjones/Muon.jl
Muon for Julia
Language:Julia1 0
dcjones/pix2pix
Image-to-image translation with conditional adversarial nets
Language:Lua1 0
dcjones/RSEM
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
Language:C++2 0
dcjones/seine-rs
A (rust)🦀 library and suite of tools for manipulating and processing the output of salmon, alevin, and alevin-fry 🐟
Language:Rust2 0
dcjones/squidpy
Spatial Single Cell Analysis in Python
Language:Python2 0
dcjones/TiffImages.jl
Pure-Julia TIFF I/O with a focus on correctness 🧐
Language:Julia2 0