mukamel-lab
We are the UCSD Computational Neural Data and Dynamics Lab (CNDD). This page hosts software for neural data ranging from imaging to sequencing.
UCSDSan Diego
Pinned Repositories
BICCN-Mouse-MOp
Analysis notebooks for BICCN mouse primary motor cortex project.
CellSort
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
EpiAttend
Single cell epigenome modeling
HumanBrainAging
single_nuclei_transcriptome_epigenome_variability
mop
Multiomics Processing
robustlink
A python package that links enhancers to genes using single-cell transcriptomes and epigenomes
SingleCellFusion
SingleCellFusion--a tool to integrate single-cell transcriptome and epigenome data
SingleCellFusion_Loompy-Obsolete
Methods for integrating multimodal single cell sequencing data, including transcriptome (RNA-Seq) and epigenome (DNA methylation, ATAC-Seq)
slavseq_browser
IGV browser for viewing slav-seq data
snmcseq
Tools for computational analysis of single nuclei methylC-Seq data, as described in Luo, Keown et al. (2017)
mukamel-lab's Repositories
mukamel-lab/CellSort
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
mukamel-lab/SingleCellFusion
SingleCellFusion--a tool to integrate single-cell transcriptome and epigenome data
mukamel-lab/snmcseq
Tools for computational analysis of single nuclei methylC-Seq data, as described in Luo, Keown et al. (2017)
mukamel-lab/EpiAttend
Single cell epigenome modeling
mukamel-lab/mop
Multiomics Processing
mukamel-lab/robustlink
A python package that links enhancers to genes using single-cell transcriptomes and epigenomes
mukamel-lab/SingleCellFusion_Loompy-Obsolete
Methods for integrating multimodal single cell sequencing data, including transcriptome (RNA-Seq) and epigenome (DNA methylation, ATAC-Seq)
mukamel-lab/BICCN-Mouse-MOp
Analysis notebooks for BICCN mouse primary motor cortex project.
mukamel-lab/HumanBrainAging
single_nuclei_transcriptome_epigenome_variability
mukamel-lab/slavseq_browser
IGV browser for viewing slav-seq data
mukamel-lab/ALLCools
Toolkit for single-cell DNA methylation analysis.
mukamel-lab/annoj_cndd
AnnoJ browser customized by Mukamel lab
mukamel-lab/BICCN2.0_Analysis_LIMS
Coordinate analyses of BICCN molecular data
mukamel-lab/clustereval
Easy clustering evaluation in MATLAB
mukamel-lab/deconSTORM
deconSTORM software for analyzing single molecule super-resolution microscopy data
mukamel-lab/deepcpg
Deep neural networks for predicting CpG methylation
mukamel-lab/methylpy
methylpy is a whole genome bisulfite sequencing analysis pipeline. It is developed by Mattew D. Schultz.
mukamel-lab/NEUG221
Neug221 seminar Fall 2023
mukamel-lab/notebooks
some ipython notebooks for myself and for sharing
mukamel-lab/scmc_tools
Tools for analysis of single cell methylC-seq (DNA methylation) data
mukamel-lab/scmdb_py_dev
Single cell methylation data browser
mukamel-lab/scmdb_py_dev_team_copy
Development version of single cell DNA methylation python browser
mukamel-lab/SingleCellFusion_EnhancerPaper
For SingleCellFusion enhancer paper
mukamel-lab/snAneu
Single cell analysis of aneuploidy
mukamel-lab/SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
mukamel-lab/storm-analysis
STORM movie analysis code
mukamel-lab/SunQuake_Nature2024_Reanalysis
Reanalysis of data from Sun et al., Nature 2024 (https://doi.org/10.1038/s41586-023-07011-6)
mukamel-lab/uskcode
Vilrus Ultimate Starter Kit (USK) Arduino Code