User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

Interactive software tool for the assignment of cell types in single-cell studies.

simplified cellranger for long-read data

Single-cell identity definition using random forest modelling and recursive feature elimination

Deep Unsupervised Single-cell Clustering (DUSC) is a hybrid approach for cell type discovery in scRNA-seq data.

Single-Cell RNA-seq analysis workflow for 10x Genomics data

An advanced computational biology project aimed at analyzing causal networks of space-induced neurodegeneration in mice using NASA's OSD-352 dataset and PC algorithm; Ultimately mapping findings to human genes for insights into neurodegenerative diseases and space health.

Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using single‑cell RNA‑seq" by Wang B. et. al, using the raw counts matrix they provide.

Reproducible R workflow that generates bulk RNA-seq from single-cell references, injects batch/biology effects, and compares correction methods (ComBat, limma, RUV, fastMNN, SVA) using quantitative metrics and plots. Outputs are bulk-level assays (bulk_counts).

Deterministic, explainable proteostasis QC for single-cell expression data

Deterministic, explainable secretion-state QC for single-cell expression data.

Deterministic ribosome and translation-state quality control for single-cell RNA-seq.

Deterministic, explainable autophagy/lysosome dependency QC for single-cell expression data.

kira-microenvironment builds a deterministic directed interaction-potential graph over groups: source_group -> ligand -> receptor -> target_group. It resolves LR resources, aggregates expression by group, scores pairwise group interactions, summarizes network structure, and can optionally link with kira-secretion regimes

kira-organelle is the aggregation and orchestration layer for the Kira organelle QC stack. It consumes the per-tool contract artifacts emitted by kira-mitoqc, kira-nuclearqc, kira-spliceqc, kira-riboqc, kira-proteoqc, kira-autolys, and kira-secretion, then produces unified machine-readable outputs and a static report.

Original scripts for the manuscript "Sex shapes cell-type-specific transcriptional signatures of stress exposure in the mouse hypothalamus", Brivio et al. Cell Reports, 2023

Deterministic splicing quality control for single-cell RNA-seq

sc-RNA-seq data analysis of cardiac development in zebrafish

In this reposity I will give you all script I created. All this script are specialised for one way : annalyse RNA-seq data.