SURGE – uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models
Genetic regulation of gene expression is a complex process, with genetic effects known to vary…
Browsing: Other Tools
FindAdapt – A python package for fast and accurate adapter detection in small RNA sequencing
Adapter trimming is an essential step for analyzing small RNA sequencing data, where reads are…
SinCMat – A single-cell-based method for predicting functional maturation transcription factors
A major goal of regenerative medicine is to generate tissue-specific mature and functional cells. However,…
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…
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…