Lightbulb

An R single cell RNA-seq analysis pipeline/suite. It focuses on the following utilities:

1. creating super cells from single cell data to fix drop out and noise of scRNA-seq
2. Annotating single cell data according bulk RNA-seq
3. Comparing temporal scRNA-seq data of different lineage/time-line, identify the key genes

Example

Example jupyter notebooks / markdown files: https://github.com/Arthurhe/Lightbulb/tree/master/Examples

Example data: https://www.dropbox.com/sh/ym6iuxwd129ryeo/AABdaxxkoEJ-K6V86KaebJvka?dl=0

Components

part name	description	progress	to-dos
Basics	basic data processing functions	partially documented	documentation
BulkAnnotation	Annotate sc data with bulk data	V0.2 documented	currently doesn't utilize the full information of bulk replicates
LineageCompare	identify gene expression pattern	undocumented	documentation
PlotSuite	Plotting functions for Seurat object	undocumented	documentation

Installation

if (!require("devtools")) install.packages("devtools")
devtools::install_github("Arthurhe/Lightbulb")

Dependency

Depends:

R (>= 3.4.4),
data.table (>= 1.12.0),
Matrix (>= 1.2-14),
Seurat (2.3.4), #currently the code is not compatible with Seurat V3+ because of data structure

Imports:

matrixStats (>= 0.54.0),
gplots (>= 3.0.1.1),
mixtools (>= 1.1.0),
fastcluster (>= 1.1.25),
RANN (>= 2.6.1),
igraph (>= 1.2.4),
GenomicRanges (>= 1.26.4),
WGCNA (>= 1.66),
rsvd (>= 1.0.0)