an integrative analysis tool for analysing large-scale single cell RNA-sequencing data

A number of functions were generated to perform pan-cancer DEG analysis, correlation analysis between gene expression and TMB, MSI, TIME, and promoter methylation. Methods for visualization were pr…

R Package: Parallel Distance Matrix Computation using Multiple Threads

R package for integrating and analyzing multiple single-cell datasets

a parallel R package for detecting copy-number alterations from short sequencing reads

A package for automated processing of single cell RNA-seq data in cancer

Spatial Transcriptomic Analysis of OSCC samples

Code from our study "Epigenetic heterogeneity and transcriptional drivers of triple-negative breast cancer"

Not just another biomarkers: Functionality for biomarker discovery

Imputing proteomics data using deep learning models

Provides Quality Control of sequencing samples by deducing if there is batch effect and adjusts for it.

RcisTarget: Transcription factor binding motif enrichment

Deep Learning Based Models for Preimplantation Mouse and Human Development

The R package scCODE, a platform for data-specific DE gene detection for scRNA-seq data

A computational method to rank and infer drug-responsive cell population towards in-silico drug perturbation using a target-perturbed gene regulatory network (tpGRN) for single-cell transcriptomic …

Code to reproduce the results from decoupleR's manuscript

R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.

R package to infer biological activities from omics data using a collection of methods.

radar charts with ggplot2

Extended tools for correlation analysis and visualization.

A Nextflow pipeline to perform quality control, alignment, and quantification of RNA sequencing data.

A Nextflow pipeline to perform peak calling of ChIP-seq, ATAC-seq or CUT&Tag sequencing data.

A Nextflow pipeline to perform quality control, alignment, and feature coverage of CUT&Tag sequencing data.

Adipose Tissue Retains an Epigenetic Memory of Obesity that Persists Weight Loss

Toolbox of the Human Neural Organoid Cell Atlas

Reproducibility repository for the Human Neural Organoid Atlas publication