A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity
Individual cells can assume a variety of molecular and phenotypic states and recent studies indicate…
Browsing: Other Tools
LAPA – analysis of alternative polyadenylation from long-read or short-read RNA-seq
Alternative polyadenylation (APA) is a major mechanism that increases transcriptional diversity and regulates mRNA abundance.…
miRPipe – a unified computational framework for a robust, reliable, and reproducible identification of novel miRNAs from RNA sequencing data
In eukaryotic cells, miRNAs regulate a plethora of cellular functionalities ranging from cellular metabolisms, and…
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells
Sophisticated methods to properly pre-process and analyze the increasing collection of single-cell RNA sequencing (scRNA-seq)…
CAPITAL – alignment of single-cell trajectory trees
Global alignment of complex pseudotime trajectories between different single-cell RNA-seq datasets is challenging, as existing…
Entropy sorting of single-cell RNA sequencing data to discern meaningful cellular heterogeneity from technical or biological noise
A team led by researchers at the Wellcome-MRC Cambridge Stem Cell Institute has developed entropy…
CellMap – in silico cell type decomposition is an efficient, inexpensive, and convenient alternative to scRNA-Seq that can leverage bulk RNA-seq
Induced pluripotent stem cell (iPSC) derived cell types are increasingly employed as in vitro model…
scIMC – a platform for benchmarking comparison and visualization analysis of scRNA-seq data imputation methods
With the advent of single-cell RNA sequencing (scRNA-seq), one major challenging is the so-called ‘dropout’…
scAllele – A versatile tool for the detection and analysis of variants in scRNA-seq
Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels.…
Cogito – automated and generic comparison of annotated genomic intervals
Genetic and epigenetic biological studies often combine different types of experiments and multiple conditions. While…