scRepertoire -- Single-Cell Immune Repertoire Analysis

scirpy -- Python toolkit for single-cell immune receptor (TCR and BCR) repertoire analysis built on the scverse ecosystem. Defines clonotypes from paired chain data using CDR3 nucleotide/amino acid se

3 shared topics • 1 shared operation

ScreenProcessing — Python pipeline for analyzing pooled genetic screens (CRISPRi/CRISPRa). Converts raw FASTQ sequencing files into library counts using fastqgz_to_counts.py, then generates sgRNA phen

2 shared topics • 2 shared operations

Alleloscope — allele-specific copy number analysis and tumor clonality inference from single-cell multi-omics data (scDNA-seq and scATAC-seq). Estimates allele-specific copy number profiles using SNP

3 shared topics

Perturb-seq analysis tools including MIMOSCA (Multi-Input Multi-Output Single-Cell Analysis) for CRISPR perturbation screens with single-cell RNA-seq readout. Handles guide RNA assignment to cells, pe

3 shared topics

Tools for manipulating next-generation sequencing data stored in SAM/BAM/CRAM format, including sorting, indexing, and format conversion.

3 shared topics