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aquarium

a way to learn javascript graphics by evolving artificial life

bigquery-visualiser

A Shiny app to visualise BigQuery data in R. Open sourced so you can deploy on your own Shiny server.

blogdown.gibbsdavidl

the blogdown source

braindecon

Using Allen scRNA-seq to generate cell signatures, and using them to deconvolve bulk expression.

bustools

Tools for working with BUS files

catterplots

Did you ever wish you could make scatter plots with cat shaped points? Now you can!

catterplotspipeline

Example of using the Google Genomics Pipeline to produce random CatterPlots.

cgcr

scratch repository for creating and sharing

cluster_prediction_work

concordanceindex

consensusclusterparallelplus

Parallelized version of the bioconductor package ConsensusClusterPlus

cwl_scatter_example

An example of a 'scatter' and 'gather' using CWL, and the google cloud.

daves_squidpy

Spatial Single Cell Analysis in Python

diffexpr

Porting DESeq2 and DEXSeq into python via rpy2

dockerexpr

My docker experiments

ecosystem-packages

Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)

examples-python

Analysis examples based on the ISB-CGC hosted TCGA data, using Python and IPython Notebooks.

examples-r

Analysis examples based on the ISB-CGC hosted TCGA data, using R and R Markdown.

fastukey

A fast alternative for Tukey's biweight estimator of mean and correlation.

fbatpie

An FBAT implementation in python that includes the rare variant test with weighting.

gamcop_pipeline

generalized gamcop pipeline components

gene_signatures

Immune Gene Signatures for single sample gene set analysis

genesignalproc

Application of graph signal processing to gene expression data.

gibbsdavidl.github.io

my very own page.

goldfish

Using an example Kalman Filter, a Goldfish finds some food.

googlepipelinesrstan

This repository contains an example of using the google genomics pipeline to fit statistical models.

graphplanet

collection of graph algorithm implementations in python as a pedological tool.

hyperstrat

An R implementation of the hypergraph partitioning algorithm described by Vazquez (http://arxiv.org/abs/0712.1365).

iatlas.modules

immune-subtype-clustering

This repo contains the code necessary to reproduce the clusters found in "The Immune Landscape of Cancer".