Issues

• 10X Example Flex V2 Data

  ArcInstitute/cyto#249 · Filter by author loverend opened on Jul 2, 2026

• Support duplicate CRISPR guide sequences as long as (anchor, guide sequence) is unique.

  ArcInstitute/cyto#241 · Filter by author Lioscro opened on Apr 7, 2026

• Output anndata directly (especially zarr!)

  developmentenhancement
  ArcInstitute/cyto#209 · Filter by author ilan-gold opened on Feb 6, 2026
  5

• allow rerun of specific steps in workflow

  ArcInstitute/cyto#185 · Filter by author noamteyssier opened on Nov 12, 2025
  

• improve task queue scheduling

  development
  ArcInstitute/cyto#182 · Filter by author noamteyssier opened on Nov 4, 2025
  

• track per-probe-barcode unmapped reads

  enhancementstatistics
  ArcInstitute/cyto#122 · Filter by author noamteyssier opened on Aug 12, 2025
  

• create a saturation command

  enhancementibu
  ArcInstitute/cyto#98 · Filter by author noamteyssier opened on Jul 29, 2025
  

• create an ibu sampling command

  enhancementibu
  ArcInstitute/cyto#97 · Filter by author noamteyssier opened on Jul 29, 2025
  

• allow multiple feature flags to cyto map and concatenate them under the hood to support additional transgenes

  enhancement
  ArcInstitute/cyto#93 · Filter by author noamteyssier opened on Jul 15, 2025
  

• support zstd outputs for ibu

  enhancementibu
  ArcInstitute/cyto#89 · Filter by author noamteyssier opened on Jul 1, 2025