README.md

In Arthurhe/Lightbulb: single cell RNA-seq analysis suite/pipeline

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)

Arthurhe/Lightbulb documentation built on April 13, 2020, 5:12 p.m.