Related papers: RNASeqR: an R package for automated two-group RNA-…
This paper introduces the R package BayesVarSel which implements objective Bayesian methodology for hypothesis testing and variable selection in linear models. The package computes posterior probabilities of the competing hypotheses/models…
Reciprocal recommender system (RRS), considering a two-way matching between two parties, has been widely applied in online platforms like online dating and recruitment. Existing RRS models mainly capture static user preferences, which have…
A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest…
Applications of single-cell RNA sequencing in various biomedical research areas have been blooming. This new technology provides unprecedented opportunities to study disease heterogeneity at the cellular level. However, unique…
Due to the sequential sample arrival, changing experiment conditions, and evolution of knowledge, the demand to continually visualize evolving structures of sequential and diverse single-cell RNA-sequencing (scRNA-seq) data becomes…
fairseq is an open-source sequence modeling toolkit that allows researchers and developers to train custom models for translation, summarization, language modeling, and other text generation tasks. The toolkit is based on PyTorch and…
RNAnet provides a bridge between two widely used Human gene databases. Ensembl describes DNA sequences and transcripts but not experimental gene expression. Whilst NCBI's GEO contains actual expression levels from Human samples. RNAnet…
This review presents how R, the popular statistical environment and programming language, can be used in the frame of proteomics data analysis. A short introduction to R is given, with special emphasis on some of the features that make R…
Cell type identification from single-cell transcriptomic data is a common goal of single-cell RNA sequencing (scRNAseq) data analysis. Neural networks have been employed to identify cell types from scRNAseq data with high performance.…
This paper describes and illustrates the functionality of the baker R package. The package estimates a suite of nested partially-latent class models (NPLCM) for multivariate binary responses that are observed under a case-control design.…
The cellular composition of the tumor microenvironment can directly impact cancer progression and the efficacy of therapeutics. Understanding immune cell activity, the body's natural defense mechanism, in the vicinity of cancerous cells is…
R has become a cornerstone of scientific and statistical computing due to its extensive package ecosystem, expressive syntax, and strong support for reproducible analysis. However, as data sizes and computational demands grow, native R…
Ecologists and evolutionary biologists are relying on an increasingly sophisticated set of statistical tools to describe complex natural systems. One such tool that has gained increasing traction in the life sciences is structural equation…
Summary: The DynaSig-ML (Dynamical Signatures - Machine Learning) Python package allows the efficient, user-friendly exploration of 3D dynamics-function relationships in biomolecules, using datasets of experimental measures from large…
Sequencing technologies have revolutionised the field of molecular biology. We now have the ability to routinely capture the complete RNA profile in tissue samples. This wealth of data allows for comparative analyses of RNA levels at…
Detecting chemical modifications on RNA molecules remains a key challenge in epitranscriptomics. Traditional reverse transcription-based sequencing methods introduce enzyme- and sequence-dependent biases and fragment RNA molecules,…
To address a looming crisis of unreproducible evaluation for named entity recognition, we propose guidelines and introduce SeqScore, a software package to improve reproducibility. The guidelines we propose are extremely simple and center…
Crossover designs are widely applied in medicine, agriculture, and other biological sciences, yet their analysis remains challenging due to longitudinal observations within each unit and the presence of carry-over effects. Despite their…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
In the rapidly evolving domain of next generation sequencing and bioinformatics analysis, data generation is one aspect that is increasing at a concomitant rate. The burden associated with processing large amounts of sequencing data has…