patrickjdanaher
Biostatistician / computational biologist. Biostats Ph.D. from UW. Long tenure at NanoString. Focus on gene expression and spatial omics.
@Nanostring-Biostats Seattle, WA, USA
Pinned Repositories
InSituType
An R package for performing cell typing in SMI and other single cell data
Insitutype-manuscript-analyses
Analyses for the manuscript, "Insitutype: likelihood-based cell typing for single cell spatial transcriptomics"
SpatialDecon
The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This algorithm also works in bulk expression profiling data.)
cell-profile-library
Library of cell type gene expression profiles for mixed cell deconvolution.
CITN07-nCounter-data-code-results
Reproducible workflow for Figure 5 of Bhardwaj et al Nat Cancer
colby
Color functions for Base graphics
dramatic-voting
An R function to cast thousands of random votes for user-specified alternatives, animating the horse-race as votes are cast.
gene-set-DE-explorer
gene set guided plotting for differential expression analyses
JGL-package
Joint Graphical Lasso R package
SpatialDecon-for-BioC
mixed cell deconvolution in spatial gene expression data
patrickjdanaher's Repositories
patrickjdanaher/dramatic-voting
An R function to cast thousands of random votes for user-specified alternatives, animating the horse-race as votes are cast.
patrickjdanaher/gene-set-DE-explorer
gene set guided plotting for differential expression analyses
patrickjdanaher/JGL-package
Joint Graphical Lasso R package
patrickjdanaher/cell-profile-library
Library of cell type gene expression profiles for mixed cell deconvolution.
patrickjdanaher/CITN07-nCounter-data-code-results
Reproducible workflow for Figure 5 of Bhardwaj et al Nat Cancer
patrickjdanaher/colby
Color functions for Base graphics
patrickjdanaher/SpatialDecon-for-BioC
mixed cell deconvolution in spatial gene expression data
patrickjdanaher/Tumor-Deconvolution-Challenge-Workflow