CellGenIT Tools

Zarr — chunked, compressed N-dimensional array storage for large numerical datasets in bioinformatics and scientific computing. Supports cloud-native storage (S3, GCS, Azure), parallel read/write, and

3 shared topics • 1 shared operation

AGAT (Another Gff Analysis Toolkit) — comprehensive Perl toolkit for reading, writing, validating, fixing, and manipulating genome annotation files in GFF3, GTF, and GFF2 formats. Converts between for

2 shared topics • 2 shared operations

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 • 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

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 • 2 shared operations