RStudio Server

Carolina Cloud’s RStudio Server is a full web-based R development environment pre-loaded with a comprehensive genomics and bioinformatics toolkit. It includes 30+ command-line tools, a full R/Bioconductor stack, and an integrated Shiny Server for building interactive applications.

Two RStudio flavors are available:

RStudio Server (rstudioserver) — Genomics-focused with samtools, GATK, STAR, Bioconductor, and more.
RStudio Geospatial (rgeospatial) — Includes geospatial R packages (sf, terra, leaflet) alongside the base RStudio environment.

Access

RStudio is accessed through your web browser at https://<instance-name>.carolinacloud.io.

Username: ccloud
Password: Shown on your instance card in the dashboard

SSH is also available for command-line work alongside the RStudio interface.

Shiny Server

Every RStudio instance includes an integrated Shiny Server on port 3838. Access your Shiny apps at:

https://<instance-name>-shiny.carolinacloud.io

Note the -shiny suffix on the subdomain. A convenient button is provided on your instance card in the dashboard.

Use RStudio’s “Run in Background” option so the Shiny app keeps running while you continue working in the R console.

S3 integration

RStudio Server supports S3 pre-fill at creation time for pulling reference genomes, datasets, or experiment results. See S3 Integration for details.

AI integration

Pass an Anthropic API key at creation time to wire up the in-IDE AI surfaces: gander (Ctrl+Shift+I addin for in-place code edits), ellmer (programmatic R chat), and shinychat (chat UI for Shiny apps). The Claude Code CLI is also pre-installed for use from the RStudio Terminal pane. See AI Integration for details.

Pre-installed tools

R packages: DESeq2, edgeR, limma, GenomicRanges, Biostrings, rtracklayer, tidyverse, ggplot2, BiocManager

Command-line tools: samtools 1.22, bcftools 1.22, GATK 4.6, STAR 2.7, bowtie2 2.5, kallisto 0.51, PLINK 2.0, beagle 5.4, GLIMPSE2 2.0, Nextflow 25.10

System: Python 3.12, Java (OpenJDK), R with full dev tools, complete build toolchain

Creating an RStudio Server

ccloud new container --cpus 16 --ram 64 --disk 500 \
  --flavor rstudioserver --tier high-performance \
  --name rstudio-genomics

For full provisioning details (dashboard, API, CLI), see the RStudio Quickstart.

Auto-stop on idle

Enable auto-stop to have your RStudio Server shut itself off after a window of idle CPU — useful if you leave a session open overnight or across weekends. Your project files, installed R packages, and Shiny apps all persist on the container’s disk.