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: Other Tools
GTax – improving de novo transcriptome assembly by removing foreign RNA contamination
The cost and complexity of generating a complete reference genome means that many organisms lack…
RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations
Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks…
SQANTI-SIM – a simulator of controlled transcript novelty for lrRNA-seq benchmark
Long-read RNA sequencing has emerged as a powerful tool for transcript discovery, even in well-annotated…
DREEP – predicting drug response from single-cell expression profiles of tumours
Intra-tumour heterogeneity (ITH) presents a significant obstacle in formulating effective treatment strategies in clinical practice.…
Researchers develop new method to identify and remove background noise from single cell data
CITE-seq (cellular indexing of transcriptomes and epitopes) is an RNA sequencing-based method that simultaneously quantifies…
scReadSim – a single-cell RNA-seq and ATAC-seq read simulator
Benchmarking single-cell RNA-seq (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) computational tools…
scTensor detects many-to-many cell–cell interactions from single cell RNA-sequencing data
Complex biological systems are described as a multitude of cell-cell interactions (CCIs). Recent single-cell RNA-sequencing…
sciCSR – infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data
Class-switch recombination (CSR) is an integral part of B cell maturation. Researchers at the University…
scDiffCom – a tool for differential analysis of cell–cell interactions from single-cell transcriptomics data
Dysregulation of intercellular communication is a hallmark of aging. To better quantify and explore changes…