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…
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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…
Digital RNA sequencing using unique molecular identifiers enables ultrasensitive RNA mutation analysis
Understanding genetic mutations is crucial for various applications, from diagnosing diseases to unraveling the complexities…
KinPred-RNA – kinase activity inference and cancer type classification using machine learning on RNA-seq data
Kinases play a pivotal role in regulating various cellular processes by transferring phosphate groups from…
TFvelo – gene regulation inspired RNA velocity estimation
Understanding the dynamics of gene expression within single cells is crucial for deciphering cell fate…
Unraveling genomic mysteries: Sniffles2 and the quest for accurate structural variant calling
In the intricate landscape of genomics, uncovering structural variations (SVs) within the genome is akin…
PERFUMES – pipeline to extract RNA FUnctional motifs and exposed structures
Up to 75% of the human genome encodes RNAs. The function of many non-coding RNAs…
scDisInFact – disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data
Single-cell RNA-sequencing (scRNA-seq) has been widely used for disease studies, where sample batches are collected…
NanOlympicsMod – benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing
N6-methyladenosine (m6A) is the most abundant internal eukaryotic mRNA modification, and is involved in the…