https://github.com/imamachi-n/bridger
An R library for comprehensive BRIC-seq data analysis
https://github.com/imamachi-n/bridger
Last synced: 3 months ago
JSON representation
An R library for comprehensive BRIC-seq data analysis
- Host: GitHub
- URL: https://github.com/imamachi-n/bridger
- Owner: Imamachi-n
- License: mit
- Created: 2015-11-05T12:00:18.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2015-12-17T02:50:27.000Z (over 9 years ago)
- Last Synced: 2025-01-21T02:08:08.928Z (5 months ago)
- Language: R
- Homepage:
- Size: 94.7 KB
- Stars: 1
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# BridgeR
An R library for comprehensive BRIC-seq data analysis tool.
BridgeR library was made under R version 3.2.2.
***
##Dependencies (Required R libraries)
data.table
ggplot2
shiny
BSDA
##Install
###Linux
```
sudo R CMD INSTALL BridgeR
```
###Windows
(1) Update the path variables on your Windows computer(64-bit)
```
C:\Program Files\R\R-3.2.2\bin
```
(2) Install BridgeR library on Command Prompt
```
R CMD INSTALL BridgeR
```
##Example
(1) Calculate RNA half-life from your BRIC-seq dataset and compare RNA half-life bwtween two conditions.
```
library(BridgeR)
files <- c("Control.fpkm_table",
"Knockdown.fpkm_table")
hour <- c(0,1,2,4,8,12)
group <- c("Control","Knockdown")
BridgeRCore(InputFiles=files,
InforColumn=4,
group=group,
hour=hour,
SelectNormFactor=T,
CutoffDataPointNumber = 4,
CutoffDataPoint1 = c(1,2),
CutoffDataPoint2 = c(8,12),
ThresholdHalfLife = c(8,12),
ModelMode="R2_selection")
BridgeRCompare(InputFile="BridgeR_5C_HalfLife_calculation_R2_selection.txt",
InforColumn=4,
group=group,
hour=hour,
ComparisonFile=group,
CutoffDataPointNumber = 4,
ModelMode="R2_selection",
Calibration=F)
```
(2) Draw RNA decay curve predicted from your BRIC-seq dataset.
```
library(BridgeR)
RPKM_ctrl <- "Control.fpkm_table"
RPKM_kd <- "Knockdown.fpkm_table"
Normalized_data <- "BridgeR_5C_HalfLife_calculation_R2_selection.txt"
group <- c("Control","Knockdown")
hour <- c(0,1,2,4,8,12)
BridgeReport(filename1=RPKM_ctrl,
filename2=RPKM_kd,
filename3=Normalized_data,
group=group,
hour=hour,
ComparisonFile=group,
SearchRow = "symbol",
InforColumn = 4,
Color = c("black","red"),
CutoffDataPoint1 = c(1,2),
CutoffDataPoint2 = c(8,12))
```