scBayes – a Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data
Genetic and gene expression heterogeneity is an essential hallmark of many tumors, allowing the cancer…
Browsing: Expression and Quantification
RedRibbon – A new rank–rank hypergeometric overlap for gene and transcript expression signatures
High-throughput omics technologies have generated a wealth of large protein, gene, and transcript datasets that…
Isoformic – Transcript Level RNA-seq Analysis for Human Data
Transcriptome analysis is a widely used method in biological sciences, providing insights into gene expression…
Population-level integration of single-cell datasets enables multi-scale analysis across samples
The increasing amount of data recorded in medical research can only lead to scientific breakthroughs…
STREAK – A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring
The accurate estimation of cell surface receptor abundance for single cell transcriptomics data is important…
DISCERN – deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection
Single-cell sequencing provides detailed insights into biological processes including cell differentiation and identity. While providing…
iDESC – identifying differential expression in single-cell RNA sequencing data with multiple subjects
Single-cell RNA sequencing (scRNA-seq) technology has enabled assessment of transcriptome-wide changes at single-cell resolution. Due…
STREAK – a supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data
The accurate estimation of cell surface receptor abundance for single cell transcriptomics data is important…
CellBender – unsupervised removal of systematic background noise from droplet-based single-cell experiments
Droplet-based single-cell assays, including single-cell RNA sequencing (scRNA-seq), single-nucleus RNA sequencing (snRNA-seq) and cellular indexing…
sccomp – robust differential composition and variability analysis for single-cell data
Cellular omics such as single-cell genomics, proteomics, and microbiomics allow the characterization of tissue and…