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Chemical Information from the Web.

Provides hurdle negative binomial models for differential expression analysis with long-read RNA-Seq data.

Implementation of the Ibex algorithm for single-cell embedding based on BCR sequences. The package includes a standalone function to encode BCR sequence information by amino acid properties or sequence order using tensorflow-based autoencoder. In addition, the package interacts with SingleCellExperiment or Seurat data objects.

toscca is an R package to perform Thresholded Ordered Sparse Canonical Correlation Analysis (TOSCCA).

This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.

XAItest is an R Package that identifies features using eXplainable AI (XAI) methods such as SHAP or LIME. This package allows users to compare these methods with traditional statistical tests like t-tests, empirical Bayes, and Fisher's test. Additionally, it includes simThresh, a system that enables the comparison of feature importance with p-values by incorporating calibrated simulated data.

Educational resource on performing RNA-seq analysis in the cloud using Amazon AWS cloud services. Topics include preparing the data, preprocessing, differential expression, isoform discovery, data visualization, and interpretation.