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RNA-seq analysis workspace

One workspace for RNA-seq data, compute, analysis, and results.

Bring in sequencing data, run a reproducible managed pipeline, and move from quality control to genes, pathways, and research-ready outputs.

Start free Explore the pipeline
Results · Liver Sample 6 samples · 2 groups · 1 DE run
Results ready
NotchBio RNA-seq results workspace showing differential-expression results and linked quality measurements.

A State of the Art Reproducible Bioinformatics Pipeline

01

Bring in the data

Start with public or sequenced reads.

Add RNA-seq samples from NCBI accessions or Illumina data, then keep every source file inside the same project.

  • Resolve SRR accessions without manual downloads
  • Import selected Illumina FASTQ files
  • Track source and readiness for every sample
02

Group samples for DE

Turn samples into a clear comparison.

Group replicates by condition, choose a baseline, and make the differential-expression design explicit before compute starts.

  • Create control and treatment groups visually
  • Keep replicates and unassigned samples visible
  • Choose the baseline that defines up and down
03

Set pipeline controls

Control every stage before the run.

Review cleanup, quantification, differential expression, and pathway settings in one run plan. Use guided defaults or open advanced controls when needed.

  • Set controls for each processing step
  • Keep tools, versions, and parameters recorded
  • Review the full plan and runtime estimate
04

Read the result

Move from compute to a readable DE result.

Inspect significant genes, sample-level QC, fold changes, and the active comparison without switching between scripts and folders.

  • Live significance and fold-change controls
  • Genes, QC context, and plots together
  • Every result linked to its input run
Differential expression DESeq2 · group 2 vs group 1
Results ready
NotchBio differential-expression overview with significant genes and linked quality measurements.
05

Explore pathway context

Follow changed genes into biology.

Rank pathway signals, inspect member genes, and open focused evidence without losing the active differential-expression comparison.

  • Ranked gene sets across supported collections
  • Leading-edge genes on the active volcano
  • Directional pathway evidence and activity views

Built for bioinformaticians & core facilities

For sequencing teams

Core facilities

Manage customer projects, data, analysis, delivery, and researcher access from one facility workspace.

Explore core facilities

For scientific teams

Researchers

Run the RNA-seq pipeline, inspect quality, compare groups, explore pathways, and prepare figures.

Explore researchers

Bring every RNA-seq dataset into one project

FASTQDirect uploadFrom your computer
BSIllumina BaseSpaceSelect project FASTQ files
BOXBoxImport shared FASTQ files
GEOPublic accessionsResolve GEO, SRA, ENA, and DDBJ datasets
NotchBio projectreads · metadata · access · analysis lineage
Try the free GEO FASTQ downloader

Organized data. Managed compute. Traceable results.

Project workspacesamples, metadata, collaborators, source filesCONTROLLED
Managed computenamed tools, requested resources, tracked parametersON DEMAND
Result recordQC, genes, pathways, figures, provenanceTRACEABLE

Ready to move from RNA-seq data to a result you can use?

Start free Book a facility demo