Archr

Use when working with OneK1K tools from the Powell Genomics Lab — the single-cell eQTL (sc-eQTL) analysis suite built around the OneK1K cohort (~1.27 million PBMCs from 982 donors). Covers the full pi

2 shared topics • 3 shared operations

Signac — R toolkit for single-cell chromatin accessibility analysis built on Seurat. Processes scATAC-seq data from 10x Genomics and other platforms. Handles fragment files, performs TF-IDF normalizat

2 shared topics • 3 shared operations

AnnData — annotated data matrices for single-cell and multi-omics analysis. Core data structure for the scverse ecosystem storing expression matrices (X) with observation metadata (obs), variable meta

2 shared topics • 2 shared operations

CellGenIT tools from the Wellcome Sanger Institute Cellular Genetics Informatics team. Suite of Python utilities for single-cell genomics including sinto (fragment file generation from BAM), cellhint

2 shared topics • 2 shared operations

Pegasus is a Python package for analyzing and visualizing large-scale single-cell and single-nucleus RNA-seq data, developed by the Broad Institute's Li Lab. Performs QC filtering, normalization, PCA,

2 shared topics • 2 shared operations