A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.

🌺 reference-free transcriptome assembly for short and long reads

integrated RNA-seq Analysis Pipeline

a fully Bayesian approach to deconvolve tumor microenvironment

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

Workflow management with Nextflow and nf-core

Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor

single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.

GenoCraft: A Comprehensive, User-Friendly Web Platform for High-Throughput Omics Data Analysis and Visualization (https://arxiv.org/pdf/2312.14249)

a web-based R shiny application that wraps DESeq2 R package

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.

single cell and bulk RNASeq analysis scripts

"Applied bioinformatics" is a course for Genetics Master Program at Genetics Department

Code base for the Grant, Morales-Nebreda, and Markov et al., “Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia” Nature (2021) paper

Dalmolin Group's workflow for pre-processing, alignment and quantification of bulk RNA-seq data

Trajectory Inference of clinical data via Multi-commodity Flow

Analysis pipeline for bulk RNA-seq data

A script used to calculate percent spliced-in (PSI) values from bulk RNA sequencing data.

An R tool to detect and correct batch-effects in gene-expression data (Microarray and bulk-RNAseq))