Single cell analysis suite
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R
src
.gitignore
DESCRIPTION
Lightbulb.Rproj
NAMESPACE
README.md

README.md

Lightbulb

A single cell RNA-seq analysis pipeline/suite currently focusing on 10X data and time series samples.

Todos:

part name description dependency language progress
LightReader_10X read and filter 10X data cellrangerRkit, data.table R Mostly finished
LightCleaner remove outlier and cap expression R Mostly finished
LightNorm normalization and spline find TSNE R Mostly finished
LightMagic R wrapper for magic Magic python finished
LightTree create lineage tree from LightNorm output Fastcluster, Matrix, optrees R stable version, need to correct the blocking function
LightDE find significantly variable gene bwteen/across lineage DTW R done
LightNet build gene interacion network and identify key gene modules WGCNA R WCGNA in tree
LightPlotSuite Plotting functions R Partial finished