shinyBioTools

A standalone R Shiny application for biological data analysis. It bundles seven analysis tools in a single shinydashboard interface: qPCR analysis, shRNA/sgRNA primer design, score normalization, drug synergy, thermal shift (DSF), and an end-to-end RNA-seq pipeline.

Features

• Real-time PCR: Analyze qPCR data with the delta-delta-CT method, with faceted / combined bar plots, melt-curve visualization, and Excel export
• Easy shRNA: Convert gene IDs (SYMBOL/Ensembl/Entrez), query the splashRNA database, and design overlapping-PCR primers for miR-30 based vectors
• Easy sgRNA: Design LentiCRISPRv2 cloning primers with customizable prefix/suffix sequences (forward and reverse)
• Score Norm: Rank-based inverse normal transformation (van der Waerden INT) with summary statistics, side-by-side histograms, and CSV export
• SynergyFinder: Drug synergy scoring with ZIP, HSA, Bliss, and Loewe models, including dose-response, 2D synergy, surface, and barometer plots
• DSF Analysis: Differential scanning fluorimetry — Tm (derivative or Boltzmann) and delta-Tm scatter plots, raw/derivative curves, reference-ligand handling, and optional chemical structures from SMILES
• RNA-seq: End-to-end DESeq2 pipeline — data upload with editable metadata, QC (PCA / sample correlation / variable-gene heatmap), Wald comparisons, volcano plots, and ORA + GSEA enrichment against MSigDB

Quick Start

Run the app from the project root (the app sources modules via relative paths):

# In RStudio: open app.R and click "Run App"
source("app.R")

Or from terminal:

Rscript app.R

The app listens on http://127.0.0.1:5005 (configured in app.R); a browser window opens automatically when launched from RStudio. Open that address in your browser if it does not.

Requirements

• R >= 4.5.0
• R packages (all directly used by the code):

Base / UI

• shiny, shinydashboard, tidyverse (includes ggplot2, dplyr, tidyr, readr, stringr, purrr, tibble, forcats), magrittr, DT, shinyjs, plotly

Real-time PCR

• readxl, writexl, janitor

shRNA / sgRNA

• Biostrings, httr, rvest

Score Norm

• (base R only)

SynergyFinder

• synergyfinder, patchwork, writexl, zip

DSF Analysis

• zip, janitor, mgcv, gratia, patchwork, DT, writexl
• Optional: rcdk (renders 2D chemical structures from SMILES in the Ligand Details view)

RNA-seq

• readxl, writexl, rhandsontable, DESeq2, ashr, corrplot, ggforce, ggrepel, clusterProfiler, msigdbr, enrichplot, future, furrr, matrixStats

Gene ID conversion

• AnnotationDbi, org.Hs.eg.db (human), org.Mm.eg.db (mouse)

Implicit dependencies (installed automatically): scales, rlang, gtable (via ggplot2), xml2 (via rvest), parallel (base).

Install packages (BiocManager::install handles both CRAN and Bioconductor packages):

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install(c(
  "shiny", "shinydashboard", "tidyverse", "magrittr", "patchwork",
  "writexl", "readxl", "janitor", "httr", "rvest",
  "zip", "mgcv", "gratia", "DT", "shinyjs", "plotly",
  "corrplot", "ggforce", "ggrepel", "future", "furrr", "matrixStats",
  "Biostrings", "AnnotationDbi", "org.Hs.eg.db", "org.Mm.eg.db",
  "DESeq2", "ashr", "clusterProfiler", "msigdbr", "enrichplot",
  "synergyfinder"
))

Note: rhandsontable is archived on CRAN; install it from the CRAN archive if needed:

install.packages("https://cran.r-project.org/src/contrib/Archive/rhandsontable/rhandsontable_0.3.8.tar.gz", repos = NULL, type = "source")

Project Layout

Sidebar item	Tab tabName	Module file
Real-time PCR	rtpcr	R/mod_rtpcr.R
Easy shRNA	shrna	R/mod_shrna.R
Easy sgRNA	sgrna	R/mod_sgrna.R
Score Norm	scorenorm	R/mod_scorenorm.R
SynergyFinder	synergy	R/mod_synergy.R
DSF Analysis	dsf	R/mod_dsf.R
RNA-seq	rnaseq	R/mod_rnaseq.R

Shared helpers live in R/utils.R; the app entry point is app.R. A manifest.json is included for deployment to Posit Connect / shinyapps.io via rsconnect::writeManifest().

Author

Hao He haohe90@gmail.com

License

MIT License