Signac

Use when working with ArchR for single-cell chromatin accessibility (scATAC-seq) analysis in R. ArchR builds Arrow-backed projects from fragment/BAM inputs, performs doublet scoring, iterative LSI, cl

2 shared topics • 3 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

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 • 2 shared operations

Cell Ranger ATAC — 10x Genomics official pipeline for processing single-cell ATAC-seq (scATAC-seq) data from raw FASTQ files to peak-barcode matrices and fragment files. Performs barcode demultiplexin

2 shared topics • 1 shared operation

Geneformer — transformer-based foundation model pretrained on ~30 million single-cell transcriptomes for context-specific gene network analysis. Supports fine-tuning for cell type classification, gene

2 shared topics • 1 shared operation