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Starred repositories

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A continually expanding collection of cancer genomics notes and data

3 1 Updated Sep 13, 2022

A list of scRNA-seq analysis tools

R 712 160 Updated Jul 6, 2025

A tool for detecting somatic variants in single cell data

Python 208 31 Updated Sep 15, 2024

Pretty timelines in R.

R 172 11 Updated Sep 27, 2024

Everything is Linkable

R 184 42 Updated Jun 14, 2023

Time series visualisation

R 260 39 Updated Feb 11, 2022

A package to make streamplots

R 186 15 Updated Apr 5, 2022

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 …

R 50 5 Updated Jun 5, 2025

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.

R 52 4 Updated Sep 17, 2024

Identification of clone-specific and cancer-selective multi-targeting therapeutic options based on single-cell transcriptomic profiles of cancer patients

HTML 12 1 Updated Feb 20, 2025

A curated list of awesome ggplot2 tutorials, packages etc.

1,673 180 Updated Jul 13, 2025

a pipeline for single cell RNA-seq data analysis

HTML 69 24 Updated Dec 11, 2023

Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.

R 56 13 Updated Feb 21, 2024

Area-Proportional Euler and Venn Diagrams with Ellipses

R 134 18 Updated Jun 28, 2025

pathfindR: Enrichment Analysis Utilizing Active Subnetworks

R 192 27 Updated Jun 15, 2025

Integrative pathway enrichment analysis of multivariate omics data

R 112 25 Updated Jul 11, 2025

Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.

R 95 19 Updated Nov 30, 2023

Analysis for 2019 submission "Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis" Schafflick1, Xu, Hartlehnert1 et. al

Jupyter Notebook 22 8 Updated Jun 17, 2021

Build and run Docker containers leveraging NVIDIA GPUs

17,401 2,041 Updated Dec 6, 2023

Docker Containers for Bioconductor

Dockerfile 83 32 Updated Jul 14, 2025

Ready-to-run Docker images containing Jupyter applications

Python 8,256 3,007 Updated Jul 7, 2025

Haplotype-aware CNV analysis from single-cell RNA-seq

R 186 25 Updated Jun 25, 2025

Utilizing single-cell omics from patients tumor to predict response and resistance.

70 17 Updated Apr 25, 2023

R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets

JavaScript 232 47 Updated Feb 27, 2024

R package for the joint analysis of multiple single-cell RNA-seq datasets

R 213 39 Updated Feb 26, 2024

A scripting and command-line front-end for GNU R

R 318 53 Updated Jul 10, 2025
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