Gibbsdavidl
Research scientist in the Shmulevich Lab at the Institute for Systems Biology.
@isb-cgc @IlyaLab Seattle, WA
Pinned Repositories
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.
ConsensusClusterParallelPlus
Parallelized version of the bioconductor package ConsensusClusterPlus
gibbsdavidl.github.io
my very own page.
Immune-Subtype-Clustering
This repo contains the code necessary to reproduce the clusters found in "The Immune Landscape of Cancer".
Ligand-Receptor-Pairs
Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
miergolf
Influence maximization
ProCoNA
Protein co-expression network analysis
SymbolicEntropySystems
using symbolic entropy to compute transfer entropy
gssnng
Gene Set Scoring on the Nearest Neighbor Graph (gssnng) for Single Cell RNA-seq (scRNA-seq) using AnnData h5ad files.
Gibbsdavidl's Repositories
Gibbsdavidl/CatterPlots
Did you ever wish you could make scatter plots with cat shaped points? Now you can!
Gibbsdavidl/Immune-Subtype-Clustering
This repo contains the code necessary to reproduce the clusters found in "The Immune Landscape of Cancer".
Gibbsdavidl/ConsensusClusterParallelPlus
Parallelized version of the bioconductor package ConsensusClusterPlus
Gibbsdavidl/CWL_scatter_example
An example of a 'scatter' and 'gather' using CWL, and the google cloud.
Gibbsdavidl/examples-R
Analysis examples based on the ISB-CGC hosted TCGA data, using R and R Markdown.
Gibbsdavidl/GeneSignalProc
Application of graph signal processing to gene expression data.
Gibbsdavidl/scPySingscore
Like singscore, but for single cell rna-seq. Made for scanpy anndata objects.
Gibbsdavidl/stan-zoo
A collection of common statistical tests implemented as Stan Bayesian regression models.
Gibbsdavidl/SymbolicEntropySystems
using symbolic entropy to compute transfer entropy
Gibbsdavidl/gibbsdavidl.github.io
my very own page.
Gibbsdavidl/Ligand-Receptor-Pairs
Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
Gibbsdavidl/Aquarium
a way to learn javascript graphics by evolving artificial life
Gibbsdavidl/blogdown.gibbsdavidl
the blogdown source
Gibbsdavidl/BrainDecon
Using Allen scRNA-seq to generate cell signatures, and using them to deconvolve bulk expression.
Gibbsdavidl/bustools
Tools for working with BUS files
Gibbsdavidl/cluster_prediction_work
Gibbsdavidl/concordanceIndex
Gibbsdavidl/daves_squidpy
Spatial Single Cell Analysis in Python
Gibbsdavidl/diffexpr
Porting DESeq2 and DEXSeq into python via rpy2
Gibbsdavidl/ecosystem-packages
Registry for scverse ecosystem packages (https://scverse.org/packages/#ecosystem)
Gibbsdavidl/GooglePipelinesRStan
This repository contains an example of using the google genomics pipeline to fit statistical models.
Gibbsdavidl/iatlas.modules
Gibbsdavidl/LabMeetingCalendar
Scripts used in generating the lab meeting schedule.
Gibbsdavidl/naive_tree
Gibbsdavidl/pyPairtreeOrchard
Grow your own pairtree orchard to produce robust fruit (i.e. make classifications).
Gibbsdavidl/PySingscore
Gibbsdavidl/readthedocs
Documentation for the ISB-CGC on Read the Docs.
Gibbsdavidl/robencla
Transforms data into robust forms and trains an ensemble of XGboost classifiers.
Gibbsdavidl/scanpy
Single-Cell Analysis in Python. Scales to >1M cells.
Gibbsdavidl/shiny_examples
R Shiny examples