andrei-stoica26.r-universe.dev

[andrei-stoica26] LISTO 0.8.0

andreistoica@foxmail.com (Andrei-Florian Stoica) — Mon, 25 May 2026 01:46:30 GMT

The implementation of a statistical framework for performing overlap assessments on lists comprising sets of strings (such as lists of gene sets) described in Stoica (2023) . It can assess overlaps of pairs of sets of strings selected either from the same universe or from different universes, and overlaps of triplets of sets of strings selected from the same universe. Designed for single-cell RNA-sequencing data analysis applications, but suitable for other purposes as well.

[bioc] scLang 1.1.3

andreistoica@foxmail.com (Andrei-Florian Stoica) — Thu, 07 May 2026 07:22:10 GMT

scLang is a suite for package development for scRNA-seq analysis. It offers functions that can operate on both Seurat and SingleCellExperiment objects. These functions are primarily aimed to help developers build tools compatible with both types of input.

[bioc] CSOA 1.3.1

andreistoica@foxmail.com (Andrei-Florian Stoica) — Wed, 06 May 2026 06:48:28 GMT

Cell Set Overlap Analysis (CSOA) is a tool for calculating per-cell gene signature scores in an scRNA-seq dataset. CSOA constructs a set for each gene in the signature, consisting of the cells that highly express the gene. Next, all overlaps of pairs of cell sets are computed, ranked, filtered and scored. The CSOA per-cell score is calculated by summing up all products of the overlap scores and the min-max-normalized expression of the two involved genes. CSOA can run on a Seurat object, a SingleCellExperiment object, a matrix and a dgCMatrix.

[bioc] GSABenchmark 1.1.0

andreistoica@foxmail.com (Andrei-Florian Stoica) — Tue, 28 Apr 2026 13:06:52 GMT

GSABenchmark is a package designed for benchmarking scRNA-seq gene set analysis (scGSA) methods. It provides both traditional and novel benchmark metrics, as well as visualization tools. Currently, GSABenchmark supports 17 scGSA methods.

[bioc] hammers 1.1.0

andreistoica@foxmail.com (Andrei-Florian Stoica) — Tue, 28 Apr 2026 13:06:50 GMT

hammers is a utilities suite for scRNA-seq data analysis compatible with both Seurat and SingleCellExperiment. It provides simple tools to address tasks such as retrieving aggregate gene statistics, finding and removing rare genes, performing representation analysis, computing the center of mass for the expression of a gene of interest in low-dimensional space, and calculating silhouette and cluster-normalized silhouette.

[andrei-stoica26] henna 0.8.4

andreistoica@foxmail.com (Andrei-Florian Stoica) — Tue, 28 Apr 2026 07:28:28 GMT

A visualization suite primarily designed for single-cell RNA-sequencing data analysis applications but well-suited for other purposes as well. It introduces novel plots to represent two-variable and frequency data and optimizes some commonly used plotting options (e.g., correlation, network, density, alluvial and volcano plots) for ease of usage and flexibility.