Sam Danziger's repositories
ADAPTSdata
Data for the ADAPTS package vignette
ADAPTS
Augments existing or de-novo cell-type signature matrices to deconvolve bulk gene expression data This package expands on the techniques outlined in Newman et al.'s 2015 Nature Methods paper: 'Robust enumeration of cell subsets from tissue expression profiles'. to allow a user to easily add their own cell types (e.g. a tumor specific cell type) to Newman's LM22 or other signature matrix.
cmonkey-python
Python port of cMonkey, a machine-learning based method for clustering
ADAPTSdata2
Data for the ADAPTS package vignette, package 2.
ADAPTSdata3
Data for the ADAPTS single cell Vignette
egrin2-tools
EGRIN2 tool chain
offYerBack
Code to access cMonkey RData objects and provide the data in a Python friendly manner.
offYerBackV2
A suite of tools to post process gene regulatory networks.
Scripts
Scripts developped over time and (sometimes) still usefull