mukamel-lab's Projects
Toolkit for single-cell DNA methylation analysis.
AnnoJ browser customized by Mukamel lab
Analysis notebooks for BICCN mouse primary motor cortex project.
Coordinate analyses of BICCN molecular data
This toolbox includes routines for using principal component analysis (PCA) and independent component analysis (ICA) to extract cellular signals from imaging data sets. A full description and validation of the method is provided in the paper, "Automated Analysis of Cellular Signals from Large-Scale Calcium Imaging Data," Neuron, 63:747 (2009): http://tinyurl.com/cellsort
Easy clustering evaluation in MATLAB
deconSTORM software for analyzing single molecule super-resolution microscopy data
Deep neural networks for predicting CpG methylation
Single cell epigenome modeling
single_nuclei_transcriptome_epigenome_variability
methylpy is a whole genome bisulfite sequencing analysis pipeline. It is developed by Mattew D. Schultz.
Multiomics Processing
Neug221 seminar Fall 2023
some ipython notebooks for myself and for sharing
A python package that links enhancers to genes using single-cell transcriptomes and epigenomes
Tools for analysis of single cell methylC-seq (DNA methylation) data
Single cell methylation data browser
Development version of single cell DNA methylation python browser
SingleCellFusion--a tool to integrate single-cell transcriptome and epigenome data
For SingleCellFusion enhancer paper
Methods for integrating multimodal single cell sequencing data, including transcriptome (RNA-Seq) and epigenome (DNA methylation, ATAC-Seq)
Single cell analysis of aneuploidy
Analysis Pipeline for Single Cell ATAC-seq
Tools for computational analysis of single nuclei methylC-Seq data, as described in Luo, Keown et al. (2017)
STORM movie analysis code
Vilrus Ultimate Starter Kit (USK) Arduino Code