One platform for sequencing data work.
Quality control, differential expression, clustering, plots and enrichment for bulk and single-cell RNA-seq, CITE-seq, TCR repertoires, Tn-seq fitness screens and proteomics, one step at a time and without writing code.
Reads count tables (CSV, TSV, TXT) for human, mouse, cattle, zebrafish, salmon and bacteria, and FASTQ files from human and mouse, which it counts first.
Introducing
2.0
The biggest release of baSeq so far. More kinds of data, every analysis a search away, and every result explained right where it appears.
All your analyses in one place.
Every project and analysis sits in the sidebar, and what you worked on last waits for you on Home.
- The sidebarYour projects and their analyses, each marked with its kind, one click from anywhere.
- ContinueHome opens on the analysis you worked on last.
- ProjectsGrouped as you work, and shared with your lab when you want.
Run any analysis without writing code.
Search for a step, fill in its settings and run it. The code is always there if you want to see it.
- The step barEvery step for your kind of data, a search away, with the next one suggested.
- Settings in plain wordsChoose what to compare from your own sample sheet.
- A result card per stepPlot, table, details and the code that made them.
Understand every gene in one click.
Click a gene in any table to see how it changed in your data, what it does, and what it works with.
- In this analysisIts fold change and each sample’s value, without leaving the table.
- What it doesFunction and domains from UniProt.
- What it works withIts closest partners from STRING.
- Across your labEvery analysis that found it, one click away in Findings.
Every result shows its plot, table and code.
Switch between them on the result card, and download any of them.
Edit a plot without code.
Drag labels and the legend where you want them, change the colours, and save.
Export a notebook, slides or a report.
A Jupyter notebook, a reproducibility package, PowerPoint or PDF, from the Export menu.
A second look at every result.
Referee checks a result in one click: replicates, design, multiple testing, thresholds and outliers.
A chat that suggests the next step.
Ask about your data, and it proposes a step you can set up in one click.
Follow a clonotype across your lab.
Click a CDR3 to see its share in every sample and the other analyses that hold it.
For the first time
Labs
For research groups. Your whole lab’s sequencing data work on one platform, from the facility’s delivery to the lab meeting.
Bring your whole lab onto one platform.
Create a lab, invite your group by email, and share projects and protocols with everyone in it.
- MembersInvite by email; people without a baSeq account make one from the link.
- Shared projectsMembers see what is shared with the lab: projects, analyses read-only, and datasets.
- One overviewThe lab’s data, findings, protocols and activity in one place.
Get facility data analysed as it arrives.
Give your sequencing facility a delivery link. Their files land in your lab’s inbox, and for bulk, Tn-seq and TCR data a saved protocol can run on them right away.
- A link, not an accountThe facility delivers through a link; they need no baSeq account.
- Registered on arrivalThe files land in your data with their sample sheet, and you get an email.
- Your protocol runsSave an analysis’s steps once, and the inbox runs them on each bulk, Tn-seq or TCR delivery.
Turn your lab’s scripts into reusable steps.
Add your R and Python scripts once, and anyone in the lab can run them as a step in an analysis.
- Your code, in the sandboxR and Python scripts run on the data at the step you are looking at.
- A step like any otherThe result becomes a step in the analysis; the data itself is not changed.
- Versioned and sharedEach script keeps its versions and shows who wrote it.
Work on the same analysis, at the same time.
Share an analysis with anyone in your lab. You see who else is in it, and every step either of you runs appears for both of you as it happens.
LPS vs control, 6 h
- Shared by emailThey can view and run steps; only you can delete the analysis or change who has it.
- See who is hereEveryone in the analysis shows in its top bar.
- Live for everyoneProgress and results reach everyone in the analysis as they happen.
- Runs in orderSteps started at the same time wait their turn, so the analysis stays in order.
Discuss results right where they live.
Comment on any result, and follow the lab’s activity in one feed.
Search everything your lab has found.
Search a gene or a phrase across every analysis you can open.
Seal your results and take them to lab meeting.
Freeze an analysis so it can’t change, then present it as slides.