Fluent BioSciences Announces Nature Biotechnology Journal Publication: Microfluidics-free Single-cell Genomics with Templated Emulsification

PIPseeker Release Notes & Archives

Release Notes


  • Support for multi-omics workflows:
    • Quantification of cell surface protein using Antibody Derived Tags (ADT)
    • Sample demultiplexing using Hash-Tag oligonucleotides (HTO)
  • Feature plots: show individual gene expression across cells in UMAP space
  • Clustering: better control of clustering parameters and sensitivity for improved rare cell type identification
  • SVG format option for saved images
  • Improvements to the summary report
  • Performance improvements: faster analysis and better resource utilization


  • Operating systems
    • Additional Linux support:
      • Centos8
      • Centos7
      • Ubuntu 22.10 – Kinetic 
      • Ubuntu 22.04 – Focal
      • Ubuntu 22.04 – Jammy
      • Ubuntu 18.04 – Bionic
      • Ubuntu 16.04 – Xenial
    • Native macOS support (no Docker installation required)
  • Performance improvements
    • Parallel processing
      • Parallelization was added to each major step of the pipeline to optimize system resource usage and reduce runtime.
    • RAM and disk space optimization
    • Recovery mode
      • Resume previous failed runs from the last completed step.
  • Command line interface
    • “pipseeker count” and “pipseeker reanalyze” renamed to “pipseeker full” and “pipseeker cells”.
  • Cell type annotation
    • Identify cell types in the processed sample.
  • Preflight checks
    • Verifies that the system has sufficient resources before starting the analysis.

Software Archives

PIPseeker 1.1.7

Linux   |   macOS   |   Windows*

*Requires Docker Installation

PIPseeker 1.0.0

Ubuntu 20.04   |   macOS*   |   Windows*

*Requires Docker Installation