Runs project-specific ONT-only FLAIR transcriptome generation, optional multi-sample combine, quantification, and post-quantification single-cell matrix recovery with recover_sc_matrix.py.
Summarizes completed long-read single-cell RNA-seq runs using deep results-style integrative writing, with emphasis on post-annotation isoform analysis, sequence-model outputs, transcript-level events, gene-function interpretation, and literature-grounded condition-specific consequences.
Uses Orthrus transcript-sequence embeddings plus pretrained regression and classification heads to predict isoform-level functional properties for one gene at a time in a persistent tmux shell session.
Draws gene-level sashimi plots from per-sample BAM files after downstream annotation by extracting group-specific cell barcodes from a Seurat object, subsetting BAMs by barcode tag, building ggsashimi input tables, and iteratively plotting one gene at a time in tmux.
Adds the merged isoform count assay and isoform UMAP from a merged isoform Seurat object into a merged gene Seurat object, then saves a new combined Seurat RDS for joint downstream gene-plus-isoform analysis.
Performs downstream cell type annotation for the project in one persistent tmux R session, including cluster UMAP review, cluster-level marker discovery for gene and isoform assays, optional automatic annotation with ScType, optional manual cluster renaming, celltype-level differential analysis, heatmaps, enrichment, and cell composition summaries.
Performs differential transcript usage analysis in one persistent tmux R session using a Seurat object with an isoform assay, including DTU FASTA preparation, pseudobulk aggregation by sample and cell type, GTF subsetting, IsoformSwitchAnalyzeR object initialization, filtering, ORF annotation, DEXSeq-based DTU testing, result export, and switch plotting for user-selected genes.
Draws gene or isoform feature expression on a chosen reduction from a Seurat RDS using SCP::FeatureDimPlot, and for repeated plotting must keep one R session open so the object is loaded once and the user can iteratively request more plots.