Loom

FLAMES — Full-Length Analysis of Mutations and Splicing for bulk and single-cell long-read RNA-seq data. R/Bioconductor pipeline for barcode demultiplexing, isoform discovery, transcript quantificatio

3 shared topics • 2 shared operations

STARsolo — ultrafast single-cell RNA-seq alignment, barcode processing, and UMI counting. STARsolo is a high-performance alternative to Cell Ranger for processing droplet-based (10x Genomics, Drop-seq

3 shared topics • 2 shared operations

WARP (WDL Analysis Research Pipelines) — Broad Institute's cloud-optimized collection of genomics pipelines written in WDL (Workflow Description Language). Covers whole-genome sequencing (WGS), whole-

3 shared topics • 1 shared operation

Use when performing single-cell QTL (sc-eQTL, sc-sQTL) mapping with SAIGE-QTL. SAIGE-QTL extends the SAIGE framework to single-cell RNA-seq data using Poisson mixed models to handle count overdispersi

3 shared topics • 1 shared operation

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 • 1 shared operation