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README.md

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)

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Single cell analysis suite

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