Loading homepage
Use when working with PROGENy or footprintR — saezlab R/Python tools for inferring pathway and transcription factor (TF) activity from omics data. PROGENy computes activity scores for 14 cancer-releva
Use with AI
Install the MCP server or CLI to instantly fetch PROGENy / footprintR documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/progenyfootprintr
CopyKAT (Copy number Karyotyping of Tumors) — R package for inferring genome-wide aneuploidy and copy number variations from single-cell RNA-seq data. Uses Bayesian segmentation to distinguish tumor (
3 shared topics
Use when working with EmptyDrops or DropletUtils — the Bioconductor R package for distinguishing real cells from empty droplets in droplet-based single-cell RNA-seq data (10x Genomics, Drop-seq, inDro
3 shared topics
Human Cell Atlas (HCA) tools — programmatic access to the HCA Data Portal, Data Coordination Platform (DCP), and matrix service for single-cell genomics datasets. Covers the hca Python CLI client, Azu
3 shared topics
Loom — HDF5-based file format and Python library (loompy) for storing and accessing large single-cell RNA-seq datasets. Supports sparse/dense matrices, row attributes (genes/features), column attribut
3 shared topics
salmon — Fast, bias-aware transcript quantification from RNA-seq data using selective alignment to the transcriptome. Supports bulk RNA-seq (mapping-based and alignment-based modes), single-cell RNA-s
3 shared topics