Load scTCR-seq or scBCR-seq data into a scRepertoire-compatible object.
npx skills add https://github.com/pwwang/immunopipe --skill screploading
Please help me install this Agent Skill. Skill: screploading Source: https://github.com/pwwang/immunopipe/tree/main/skills/screploading Command: npx skills add https://github.com/pwwang/immunopipe --skill screploading
Load scTCR-seq or scBCR-seq data from diverse formats into a scRepertoire-compatible object, unifying immune receptor contigs with single-cell RNA data for integrated analyses.
Provide a sample metadata file with TCRData or BCRData paths and run the screploading step to create a scRepertoire-compatible object.
High-intent search queries and answers about installing and using this skill.
To load scTCR-seq data into a scRepertoire-compatible object, provide a sample metadata file containing TCRData paths and run the screploading step to unify VDJ contigs with scRNA-seq data.
Yes, you can load scBCR-seq data from AIRR, MiXCR, and other diverse formats like 10x Genomics, BD, Dandelion, and TRUST4 into a scRepertoire-compatible object using this configuration-driven loading workflow.
The best way to integrate immune receptor contigs with scRNA-seq data is by loading scTCR-seq or scBCR-seq data from diverse formats into a scRepertoire-compatible object for unified downstream analysis.
Yes, the scRepertoire loading workflow supports ParseBio and Immcantation formats, alongside WAT3R, Omniscope, and others, reading VDJ contigs to produce a ready-to-analyze object.
To auto-enable the loading workflow, configure your sample metadata to contain TCRData or BCRData file paths, which triggers the ScRepLoading settings to automatically parse and load the immune receptor contigs.
After loading VDJ contigs into a scRepertoire-compatible object, you can perform downstream clonotype analysis and integrate the immune receptor data directly with your scRNA-seq results across platforms.
PancrePal-xiaoyibaoAutomate end-to-end scRNA-seq analysis from raw CellRanger outputs to visualization.
pwwangIntegrate TCR/BCR repertoires with scRNA-seq data to enrich Seurat metadata with clonotype information.
danilomongeRuns nf-core/airrflow immune-repertoire analysis from raw reads or assembled data.
ya-wayIntegrate single-cell TCR/BCR data with gene expression using scirpy.
