Setting Up for Experimental Success: Exploring the Importance of Pilot Studies

PIPseeker Release Notes & Archives

Release Notes


  • Merging PIPseeker results: PIPseeker merge
  • RAM and disk space optimization


  • v5 chemistry support
  • Alignment classification: exons vs. introns
  • Generating mapping references: PIPseeker buildmapref
  • Extracting specific gene expression data: PIPseeker extract
  • ADT-only workflow
  • RAM and disk space optimization


  • Minor patch to Docker image for running with limited user permissions


  • Automatic check for PIPseeker updates
  • Build cell type annotation references from PIPseeker results
  • Generate barcode whitelist from FASTQ files for custom analysis: PIPseeker barcode


  • 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 3.0.5

Linux   |   macOS (Intel)   |   MacOS (Silicon) | Windows*

*Requires Docker Installation

User Guide

PIPseeker 2.1.4

Linux   |   macOS   |   Windows*

*Requires Docker Installation

User Guide

PIPseeker 1.1.7

Linux   |   macOS   |   Windows*

*Requires Docker Installation

User Guide

PIPseeker 1.0.0

Ubuntu 20.04   |   macOS*   |   Windows*

*Requires Docker Installation