Issues

• Assess relevance of Apple container

  Reed-CompBio/spras#508 · Filter by author agitter opened on Aug 7, 2026
  1

• Sharing resources with nf-core/diseasemodulediscovery

  Reed-CompBio/spras#507 · Filter by author agitter opened on Jul 25, 2026

• unpack_singularity builds and immediately discards an intermediate SIF

  Reed-CompBio/spras#506 · Filter by author agitter opened on Jul 24, 2026

• Apptainer build fails in CHTC

  Reed-CompBio/spras#505 · Filter by author agitter opened on Jul 24, 2026

• Consider using more than the top 2 PCs for the KDE part of the PCA-based representative parameter selection

  tuning
  Reed-CompBio/spras#504 · Filter by author ntalluri opened on Jul 23, 2026
  1

• Enable Zenodo archiving

  Reed-CompBio/spras#503 · Filter by author agitter opened on Jul 17, 2026
  1

• ISMB 2026 tutorial feedback

  Reed-CompBio/spras#502 · Filter by author agitter opened on Jul 12, 2026
  1

• Improve version number updating in pre-release process

  Reed-CompBio/spras#501 · Filter by author agitter opened on Jul 10, 2026

• Updating dummy_mode defaults for OI1 (code and documentation)

  Reed-CompBio/spras#499 · Filter by author ntalluri opened on Jul 10, 2026

• Pytest only working from test/

  Reed-CompBio/spras#496 · Filter by author ntalluri opened on Jul 9, 2026
  1

• SIGMA

  algorithm
  Reed-CompBio/spras#495 · Filter by author agitter opened on Jun 29, 2026

• Automating Singularity builds from a repository commit in CHTC

  Reed-CompBio/spras#493 · Filter by author agitter opened on Jun 26, 2026

• Pelican for OSDF and Running in OSPool

  Reed-CompBio/spras#492 · Filter by author jhiemstrawisc opened on Jun 24, 2026
  1

• Immutable file feature breaks HTCondor/container runs with KeyError on hashed dataset labels

  Reed-CompBio/spras#491 · Filter by author jhiemstrawisc opened on Jun 22, 2026
  1

• Hierarchical clustering color palette

  Reed-CompBio/spras#490 · Filter by author agitter opened on Jun 16, 2026

• Add override mechanism for Cytoscape container

  Reed-CompBio/spras#482 · Filter by author agitter opened on Jun 6, 2026
  1

• Failure to run with fresh spras environment

  bug
  Reed-CompBio/spras#476 · Filter by author jhiemstrawisc opened on May 27, 2026
  1

• OrbStack as an alternative to Docker Desktop for Mac users

  Reed-CompBio/spras#472 · Filter by author ntalluri opened on May 7, 2026

• Review Queue For Two Stage Parameter Tuning

  Reed-CompBio/spras#466 · Filter by author tristan-f-r opened on Mar 26, 2026

• evaluation_pca_chosen/evaluation_per_algo_pca_chosen rules read undeclared pathway files causing fatal errors with HTCondor

  bug
  Reed-CompBio/spras#463 · Filter by author jhiemstrawisc opened on Mar 11, 2026
  5

• Update contributing guide to demonstrate typed PRA#run

  documentation
  Reed-CompBio/spras#456 · Filter by author agitter opened on Jan 9, 2026

• DENetwork

  algorithm
  Reed-CompBio/spras#455 · Filter by author agitter opened on Dec 27, 2025

• Flaky PCA test

  buginfrastructure
  Reed-CompBio/spras#452 · Filter by author tristan-f-r opened on Dec 8, 2025
  

• Potential new summary statistics

  discussion
  Reed-CompBio/spras#440 · Filter by author ntalluri opened on Nov 13, 2025

• NetworkAnalyst, another tool for pathway reconstruction

  discussion
  Reed-CompBio/spras#439 · Filter by author ntalluri opened on Nov 13, 2025
  1