Data & Analytics

Load when computing RNA velocity vectors on a scRNA AnnData with spliced / unspliced layers

Load when generating spliced / unspliced layers from Cell Ranger BAM, FASTQ, STARsolo output,

Load when an external single-cell h5ad/h5/loom/mtx needs to be canonicalised onto the OmicsClaw

Load when computing per-cell QC metrics (n_genes, total counts, mt%, ribo%) on a single-cell

Load when ordering cells along a developmental trajectory in a normalised scRNA AnnData via

Load when normalising QC'd scRNA into a PCA-ready AnnData via scanpy / Seurat / SCTransform

Load when classifying perturbed vs non-perturbed cells in a Perturb-seq / CRISPR-screen scRNA

Load when attaching cell-barcode → sgRNA assignments from a mapping TSV/CSV onto a Perturb-seq

Load when computing per-cell pathway / gene-set scores on a normalised scRNA AnnData via

Load when merging multiple single-sample scRNA-seq count matrices (one per sample-from-sc-count)

Load when aggregating single cells into metacells (sample-aware coarse-grained pseudo-cells)

Load when ranking cluster-level marker genes from a clustered single-cell AnnData via Scanpy

Load when running a single batch-correction representation (none/Harmony/Scanorama/scVI)

Load when predicting in-silico gene knockout effects on a normalised scRNA AnnData via GRN-based

Load when inferring TF → target gene regulatory networks on a normalised scRNA AnnData via

Load when extracting gene programs (NMF / cNMF factorisation) and per-cell program usage

Load when removing low-quality cells and lowly-detected genes from a single-cell AnnData

Load when checking raw single-cell FASTQ read quality (Phred / GC / adapter / length) before

Load when running bulk-style pathway enrichment (ORA / GSEA / GSEA-R / GSVA-R) on a per-group

Load when scoring drug sensitivity per cluster on an annotated scRNA AnnData via simple-correlation

Load when annotating putative doublets in single-cell RNA-seq using Scrublet, DoubletDetection,

Load when testing whether cell-type / cluster proportions or neighbourhood densities differ

Load when finding marker genes per cluster or comparing condition expression in single-cell

Load when computing per-cell differentiation potency / stemness scores from gene-expression