VISION

CytoTRACE -- computational method for predicting relative differentiation state of cells from single-cell RNA-seq data. Uses gene counts (number of detectably expressed genes per cell) as a robust pro

3 shared topics

DecontX — R/Bioconductor method in the celda package for estimating and removing ambient RNA contamination from droplet-based single-cell RNA-seq data. Uses a Bayesian Dirichlet mixture model over cel

3 shared topics

DRAGEN (Dynamic Read Analysis for GENomics) — Illumina's FPGA-accelerated bioinformatics platform for secondary analysis of next-generation sequencing data. Performs hardware-accelerated mapping, alig

3 shared topics

HTSeq — Python framework for high-throughput sequencing data analysis, primarily used for counting aligned reads overlapping genomic features (genes, exons) from SAM/BAM/CRAM files using GTF/GFF annot

3 shared topics

Scrublet — Python toolkit for computational identification of cell doublets in single-cell RNA-seq data. Simulates synthetic doublets from observed transcriptomes and scores cells via k-nearest-neighb

3 shared topics