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ArchR

ANALYTICS
Velocity0.0

Analyzing single-cell regulatory chromatin in R.

github.com/GreenleafLab/ArchR ↗

ArchR returns after three years, mostly to catch up with the ecosystem around it.

single-cellatac-seqbioinformaticsr-packagemaintenance
◆Current state
ArchR analyses single-cell chromatin accessibility data, and until early 2025 its last release was from 2022. Release 1.0.3 collects roughly three years of accumulated pull requests: ggplot2 3.5 compatibility, Seurat v5 object creation, large-matrix handling via ARMA_64BIT_WORD, trajectory and module-score work, and a published Docker image. The release candidate before it did nothing but lift a 500 MB import ceiling.
◆Where it's heading
This is a maintenance restart rather than a new direction. The contributor list shifts visibly from the original authors toward newer maintainers handling compatibility work, and the Docker image suggests an acknowledgement that reproducing the environment had become the harder problem. Whether the cadence recovers is not something these entries answer.
◆Prediction
The entries do not support a confident call on future direction; the immediate question is whether releases resume at a normal interval or 1.0.3 was a one-off catch-up.

◆Recent moves

  1. 1y ago

    Three years of fixes, Seurat v5 support and a Docker image

    Three years of merged work released at once: ggplot2 3.5 and Seurat v5 compatibility, large-matrix support, trajectory heatmaps, module scores, negative correlations and a rocker-based Docker image. Broad and long-awaited, but framed by its own notes as bug fixes and compatibility rather than new capability.

    View source ↗
  2. 1y ago

    Release candidate lifting the 500 MB S4 import limit

    A release candidate whose single change lets S4 package imports exceed 500 MB. Superseded three weeks later by the 1.0.3 release itself.

    View source ↗
  3. 4y ago

    Stability fixes and improved multiome import

    Stability work, small feature additions across many functions and improved multiome data import. The last release before the three-year gap.

    View source ↗
  4. 5y ago

    Introduces multi-omic functionality

    Stability updates driven by user feedback, and the introduction of multi-omic functionality. The multiome thread that 1.0.2 then refined starts here.

    View source ↗