Spatial transcriptomics pipeline, release p1.1
phalaena:pipeline:PA-PL-transcriptomics-spatseq
Spatial transcriptomics on 10x Visium and Visium HD inputs. The pipeline is 10x-native: Slide-seq, Stereo-seq, Curio Seeker, and Xenium-style imaging-based spatial are out of scope and route to a "talk to us" path at the bench submit surface rather than failing at validate-time. The rationale matches cellseq: 10x Visium and Visium HD dominate spatial transcriptomics by the same 75-85 percent share that 10x Chromium holds in scRNA-seq (CZ CELLxGENE Census; scTrends, Cell Genomics 2024). Pipeline ID transcriptomics_spatseq. Source: phalaena_backend/pipelines/2.3_transcriptomics_spatseq/. API entry: phalaena_api/app/pipelines/transcriptomics_spatseq.py.
- kind
- pipeline
- status
- reviewed
- github:phalaena-automata/monorepo/phalaena_backend/pipelines/2.3_transcriptomics_spatseq
View Spatial transcriptomics pipeline, release p1.1 on the Phalaena Wiki