SPADE – spatial deconvolution for domain specific cell-type estimation
In genomics, understanding how genes are expressed in different cell types within their spatial context…
Browsing: Analysis Pipelines
mAFiA – detecting m6A at single-molecular resolution via direct RNA sequencing and realistic training data
Unraveling the mysteries of RNA has always been a challenging task, but recent advancements in…
TDEseq – temporal gene expression patterns from multi-sample multi-stage single-cell transcriptomics data
Understanding how genes behave over time is crucial for unlocking the secrets of development, disease…
Procrustes – a machine-learning approach that removes cross-platform batch effects from clinical RNA sequencing data
In personalized oncology, gene expression profiling has become increasingly vital for tailoring treatment strategies to…
Improved RNA stability estimation through Bayesian modeling reveals insights into RNA decay rates
Gene expression, the process by which information encoded in DNA is translated into functional molecules…
Making the right choice! – How software is heavily influencing your omics research results and reproducibility.
Choosing the right software for RNA sequencing (RNA-seq) analysis is as important as designing the…
Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq
Understanding how genes are expressed and regulated is essential for unraveling the mysteries of life.…
SegPore – raw signal segmentation for estimating RNA modifications and structures from Nanopore direct RNA sequencing data
Estimating RNA modifications from Nanopore direct RNA sequencing data is an important task for the…
ScRAT – phenotype prediction from single-cell RNA-seq data using attention-based neural networks
Understanding the cellular basis of disease phenotypes is crucial for developing targeted therapies. Traditional bulk…
LR Hunting – a random forest based cell–cell interaction discovery method for single-cell gene expression data
Cell-cell interactions (CCIs) and communication (CCC) play vital roles in orchestrating complex biological systems. Understanding…