starxian / csbb-shiny

Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis

CSBB-Shiny

Computational Suite for Bioinformaticians and Biologists (CSBB), is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis. CSBB powered by RShiny is packed with 8 modules Visualization, Normalization, Basic Stats, Differential Expression, Correlation Profiles, Function/Pathway Enrichment, ChIP-ATAC Seq and Single Cell RNA-Seq analysis. These modules are designed in order to help researchers design a hypothesis or answer research questions with little or no expertise in Bioinformatics. CSBB is also available as a command line application and has Next generation sequencing data processing capabilities. New modules and functionalities will be added periodically

Run CSBB-Shiny from your R console or RStudio with one command

Open your R console or RStudio and paste the commands provided below. CSBB-Shiny will automatically install all required dependencies (R packages).

library(shiny)
runGitHub("CSBB-Shiny", "praneet1988", launch.browser = TRUE)

In case R package shiny is not installed please run the following command.

install.packages("shiny", repos="http://cran.us.r-project.org")
library(shiny)

Dependencies

library(shiny)
library(servr)
library(ggplot2)
library(pheatmap)
library(M3C)
library(RUVSeq)
library(scales)
library(dtwclust)
library(dplyr)
library(ggcorrplot)
library(tibble)
library(ReactomePA)
library(org.Hs.eg.db)
library(org.Mm.eg.db)
library(AnnotationDbi)
library(EnhancedVolcano)
library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(TxDb.Mmusculus.UCSC.mm9.knownGene)
library(clusterProfiler)
library(Seurat)
library(cowplot)
library(scater)
library(hdf5r)
library(DESeq2)
library(MAST)

End to End Pipeline Workflow with CSBB

Video Tutorial

https://youtu.be/c0P7TMu_IyY

Single Cell Transcriptomics Analysis Tutorial

https://www.youtube.com/watch?v=s8Q4o1e-f1E

CSBB Single Cell Browser Tutorial

https://www.dropbox.com/s/9po853gc5gzdxnl/CSBB-Shiny_scRNA_Browser.mov?dl=0