Salmon
v1.10.3 - defaultQuasi-mapping against a reference transcriptome. Fast, accurate, and the right call for most experiments.
library type - ISR (auto)
GC bias correction - on
bootstraps - 30
RNA-seq analysis you can trust, visualize, and publish faster.
Run complete RNA-seq workflows with trusted tools, customizable analyses, and publication-ready results - without setup, scripts, or infrastructure.
NotchBio
Projects My Uploads Docs
Mouse Liver RNA-Seq Experiment
Ready to runBulk RNA-seq analysis workspace for sample setup, execution, and results.
6 samples 2 groups 0 DE runs
Samples
Upload and annotate data
Run
Launch or monitor analysis
Results
Review outputs and findings
Results overview
Tune thresholds, inspect genes, and explore the plots interactively.
Primary: GroupInput: Salmon Run 1Design: ~ groupComparison: 1 vs 2
Visualizer controls
Gene report: IFITM1
16,119
Total Genes
8
Significant (padj c <= 0.050)
~ 3
Upregulated
~ 5
Downregulated
Differential expression Clustering GSEA Pathway analyses
Volcano Plot Controls
MA Plot Controls
Differential Expression
Gene: IFITM1
Gene in Comparison
Gene: IFITM1
A complete RNA-seq pipeline in one workspace.
Mouse Liver RNA-Seq Experiment
Add samplesBulk RNA-seq analysis workspace for sample setup, execution, and results.
6 samples 2 groups 0 DE runs
Upload Files Import from NCBI Add Samples
Prepare samples for analysis
Assign every sample to a group, and confirm at least two groups are represented.
SAMPLES: 6 UNASSIGNED: 0 GROUPS: 2 Continue to run
| Sample Name | Size | Type | Group | Cell line |
|---|---|---|---|---|
| SRR36938853 | 2.81 GB | FASTQ | Control | A549 |
| SRR36938854 | 1.97 GB | FASTQ | Control | A549 |
| SRR36938855 | 2.43 GB | FASTQ | Control | A549 |
| SRR36938856 | 1.98 GB | FASTQ | Treatment | A549 |
| SRR36938857 | 2.14 GB | FASTQ | Treatment | A549 |
| SRR36938858 | 2.32 GB | FASTQ | Treatment | A549 |
Mouse Liver RNA-Seq Experiment
Ready to runBulk RNA-seq analysis workspace for sample setup, execution, and results.
6 samples 2 groups 0 DE runs
Upload Files Import from NCBI Add Samples
Recommended
Balanced trimming for most bulk RNA-seq datasets.
Sensitive
More aggressive cleanup for noisy libraries.
Minimal trimming
Keep reads close to raw input with only basic filtering.
Trim preview - across 6 samples
Mouse Liver RNA-Seq Experiment
Ready to runBulk RNA-seq analysis workspace for sample setup, execution, and results.
6 samples 2 groups 0 DE runs
Upload Files Import from NCBI Add Samples
STAR
v2.7.11bSplice-aware genome alignment when you need BAM files or novel-junction discovery.
2-pass mode - off
min splice overhang - 8
output - BAM + counts
Reference
GRCh38.p14
Species
Homo sapiens
Library
Paired-end - stranded
Mouse Liver RNA-Seq Experiment
Ready to runBulk RNA-seq analysis workspace for sample setup, execution, and results.
6 samples 2 groups 0 DE runs
Upload Files Import from NCBI Add Samples
Group / Condition
Primary treatment, condition, or experimental group.
6/6 assigned - 2 levels
Cell line
Control for cell line or genetic background differences.
6/6 assigned - 1 level
Blocking variables
Cell line
Control for cell line or genetic background differences.
Design formula
~ cell_line + group
Mouse Liver RNA-Seq Experiment
Ready to runBulk RNA-seq analysis workspace for sample setup, execution, and results.
6 samples 2 groups 0 DE runs
Upload Files Import from NCBI Add Samples
Gene sets
MSigDB Hallmark
50 sets GO Biological Process
7,842 sets Reactome
1,654 sets KEGG
348 sets Permutation type
gene_set phenotype
Scoring metric
signal2noise
Mouse Liver RNA-Seq Experiment
CompletedBulk RNA-seq analysis workspace for sample setup, execution, and results.
6 samples 2 groups 0 DE runs
Upload Files Import from NCBI Add Samples
16,119
Total genes
412
Significant (p-adj < 0.05)
248
Upregulated
164
Downregulated
Differential expressionClusteringGSEAPathway analyses
Volcano plot
ControlsMA plot
ControlsDifferential expression
ControlsGene in comparison
ControlsResearch path
Designed for trusted results, flexible visuals, and faster research.
Three things matter for an RNA-seq tool: the methods, the figures, and the path from raw data to interpretation.
Benchmark-backed
Trust
Results you can stand behind
Workflows use standard methods reviewers already trust. Every run records exact tool versions and parameters.
DESeq2
v1.42.0 Salmon
v1.10.3 fastp
v0.23.4 STAR
v2.7.11b Publication-ready
Customize
Plots you can shape, then export
Adjust labels, thresholds, gene callouts, palettes, and legend placement before downloading the figure and source table.
PNG SVG PDF CSV
Managed compute
No setup
Analysis without environment pain
Skip package conflicts, tutorials, and compute provisioning. Open the workspace, attach data, configure the run.
$ pip install ...
$ conda env create ...
$ docker run ...
// not your job anymore
Compute pool
healthy - 4 nodes Workflow
Built around real RNA-seq workflows.
Configure the experiment, pick the processes you need, and run with tools and outputs your team already understands.
Sources & options
FASTQ upload Count matrix SRA / GEO import Sample metadata Paired or single-end Replicate setup
Drag in FASTQ files or paste an accession
GSE183852 - SRP345670 - PRJNA1108812
Pick a reference genome and species
GRCh38 - GRCm39 - custom transcriptome
Annotate samples with metadata
group - condition - cell line - replicate - batch
Sample sheet
6 samples - 2 groups| sample | group | condition | cell line | rep |
|---|---|---|---|---|
| SRR15278 | Control | Untreated | A549 | R1 |
| SRR15279 | Control | Untreated | A549 | R2 |
| SRR15280 | Control | Untreated | A549 | R3 |
| SRR15281 | Treatment | Drug A | A549 | R1 |
| SRR15282 | Treatment | Drug A | A549 | R2 |
| SRR15283 | Treatment | Drug A | A549 | R3 |
Tools we wire together
fastp
QC + adapter trimming
- Sliding-window trim
- Poly-G / Poly-X removal
- Per-base quality
Salmon
Transcript quantification
- Quasi-mapping
- GC bias correction
- Library auto-detect
STAR
Splice-aware alignment
- BAM + counts
- 2-pass option
- Junction discovery
DESeq2
Differential expression
- Replicate-aware
- Shrinkage estimators
- Multi-factor contrasts
GSEA
Pathway analysis
- MSigDB / GO
- Leading edge
- Activation matrix
Build the contrast
REFERENCE GROUP
Control - Untreated A549
3 replicates
COMPARE AGAINST
Treatment - Drug A 3 reps
Treatment - Drug B 3 reps
BLOCKING / COVARIATES
batchsexcell line
What this gives you
Replicate-aware comparisons
DESeq2 models batch effects and replicate structure automatically.
Multi-group contrasts
Treatment-vs-control, drug-A-vs-drug-B, and interaction terms in one run.
Cell-line and condition grouping
Metadata follows every downstream plot and table.
Reproducible re-runs
Change one parameter and a new versioned run is forked. Nothing is overwritten.
Cutoffs & comparisons
log2FC cutoff
>= 1.0 Adjusted p-value (FDR)
< 0.05 Min base mean
>= 10 Shrinkage
apeglm Top significant genes
n = 412 sig genelog2FCp-adjdir
MX1 +5.32 1.2e-22 up
IFI6 +4.81 8.4e-19 up
ISG15 +4.49 3.1e-18 up
OAS1 +3.92 2.7e-16 up
BCL2 -3.74 5.5e-14 down
MYC -3.41 9.8e-13 down
FOXO3 -2.95 1.4e-11 down
Everything generated by a run
PCA plot
PNG / SVG / PDF / CSV
Volcano plot
PNG / SVG / PDF / CSV
Heatmap
PNG / SVG / PDF / CSV
MA plot
PNG / SVG / PDF / CSV
QC report
PNG / SVG / PDF / CSV
Gene table
PNG / SVG / PDF / CSV
DE results
PNG / SVG / PDF / CSV
GSEA bundle
PNG / SVG / PDF / CSV
Run parameters
PNG / SVG / PDF / CSV
Customize every plot before you export.
The plots in the workspace are the same ones you'll ship in a paper. Tune thresholds, labels, and colors, then export at the resolution you need. The underlying table downloads with every figure.
Volcano
PNG SVG PDF CSV
PCA
PNG SVG PDF CSV
Heatmap
PNG SVG PDF CSV
MA plot
PNG SVG PDF CSV
Gene expression
PNG SVG PDF CSV
Outputs
Outputs ready for analysis, sharing, and publication.
Every run produces a versioned bundle of tables, plots, reports, and parameters you can inspect in the workspace or download as a package.
run_2026-05-15_idh1-vs-ctrl
6 samples - 412 sig genes - 28 enriched pathways
QC_Report.pdf 2.4 MB
Differential_Expression.csv 1.1 MB
Volcano_Plot.svg 84 KB
PCA_Plot.png 412 KB
Heatmap.pdf 1.7 MB
MA_Plot.svg 61 KB
GSEA_Results.csv 320 KB
Run_Parameters.json 6 KB
Workflow_Log.txt 48 KB
Differential expression tables
Clean gene-level results with fold change, p-values, FDR, and significance flags.
QC reports
Per-sample quality summaries and processing metrics so you can validate the run before interpretation.
Visualization exports
PCA, volcano, MA, heatmap, GSEA, and gene-expression plots with vector exports.
Analysis summary & run log
Parameters, comparisons, tool versions, and execution traces captured for every run.
Project workspace
Inputs, runs, comparisons, and outputs organized in one place.
Workspace
Everything your RNA-seq workspace needs.
Past the pipeline, NotchBio is a real workspace: parameters, runs, plots, files, and people, all in one place.
Managed compute
Elastic CPU and memory pools. The platform spins up the right size for your run.
Guided workflows
Step through inputs, QC, quant, design, and DE with sensible defaults at every fork.
Configurable parameters
Override anything you need: trimming thresholds, library type, contrasts, shrinkage.
Versioned runs
Each run captures inputs, parameters, tool versions, and outputs as a frozen record.
Interactive results
Pan, zoom, filter, and label inside the browser before you decide what to export.
Export-ready bundles
Tables, reports, plots, and JSON parameters in one zip. Drop straight into a paper.
Team workspaces
Invite collaborators with role-based access. Comments and run history stay with the project.
Secure projects
Projects are isolated, encrypted at rest, and access-controlled at the project level.
Use cases
Built for teams that need RNA-seq results faster.
The shape of an RNA-seq workspace varies by team. NotchBio carries the same pipeline across the contexts that matter most.
Academic labs
Standardize analysis across the lab
Lab members run the same workflow, get the same plot styles, and ship comparable results. Onboarding a new grad student takes an afternoon, not a semester.
- Shared project templates
- Per-student workspaces
- Reproducible methods section
Biotech teams
Get to biological interpretation faster
Sequencing data lands in NotchBio and comes out as DE tables and pathway maps the same day. No internal pipeline team required.
- SLA-friendly turnaround
- Audit-ready run history
- Custom contrasts per experiment
Core facilities
Deliver repeatable outputs to clients
Run dozens of projects from the same workspace, branded reports, and predictable deliverables. Charge per project, not per support ticket.
- Project isolation per client
- White-labeled exports
- Per-project billing
Consultants
Run client projects without overhead
Drop in FASTQ, configure the contrast, export a deliverable. The pipeline isn't your product, the analysis is.
- No infra to maintain
- Versioned client runs
- Professional deliverables
Research teams
Explore conditions, compare cohorts
Compare across treatments, time points, and cell lines. Customize figures and drop them straight into a paper draft.
- Multi-group contrasts
- Per-figure customization
- Paper-ready vectors
Security
Secure by design for research data.
Built for the way labs and biotech teams actually want to handle data: isolated workspaces, encrypted storage, and records that hold up to internal review.
User / team
Project workspace
Analysis run
Results storage
encrypted at rest - TLS in transit RBAC - audit trail - isolated compute
Project isolation
Each analysis workspace keeps files, runs, and outputs separated. Nothing leaks across projects.
Data ownership
Uploaded data and generated results remain yours. We provide the software layer, not your IP.
Controlled access
Invite only the people who should be on a project, with role-based permissions.
Secure cloud storage
Encrypted at rest, encrypted in transit. Computation is isolated per project.
Reproducible records
Every run captures parameters, workflow versions, and tool versions for full traceability.
Turn RNA-seq data into trusted, publication-ready results.
Upload your data, run a complete workflow, customize your visuals, and export everything your research needs.
Complete pipeline Managed compute Customizable plots Export-ready results Secure workspace