This package removes unwanted variation from raw sequencing count data using Negative Binomial and/or Zero Inflated Negative Binomial model. Thus far, the package has been applied to remove unwanted variation from single-cell RNA-seq and shotgun metagenomics data. The package takes raw sequencing count as input and thus in principle can be appli…
☆18Jun 13, 2024Updated last year
Alternatives and similar repositories for ruvIIInb
Users that are interested in ruvIIInb are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Regulatory networks with Direct Information☆18Oct 14, 2019Updated 6 years ago
- My notes/usage examples for various Bioconductor packages☆15Jan 9, 2017Updated 9 years ago
- MarcoPolo is a clustering-free approach to the exploration of bimodally expressed genes along with group information in single-cell RNA-s…☆21Nov 17, 2024Updated last year
- Automated marker-based annotation of cell types☆14Aug 8, 2022Updated 3 years ago
- Instructions and analysis scripts for single cell Higher Order Testing (scHOT)☆10Oct 7, 2020Updated 5 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- ☆19Jun 5, 2024Updated last year
- ☆29Sep 4, 2023Updated 2 years ago
- Optimal distance lower bound k-mer sampling.☆12Jun 19, 2024Updated last year
- scMalignantFinder is a Python package specially designed for analyzing cancer single-cell RNA-seq datasets to distinguish malignant cells…☆18Mar 27, 2026Updated last month
- Source code and data supporting "Evaluating measures of association for single-cell transcriptomics"☆17Feb 25, 2019Updated 7 years ago
- Information-based dimensionality reduction☆29Dec 14, 2024Updated last year
- Spatial Image Analysis of Tissues☆15Dec 8, 2022Updated 3 years ago
- Iterate k-min-mers from a DNA sequence in Rust☆13Apr 8, 2024Updated 2 years ago
- Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Gen…☆40May 6, 2022Updated 4 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆11Jan 7, 2020Updated 6 years ago
- GIANT (Gene-based data Integration and ANalysis Technique) is a method for large-scale joint analyses of atlas-level single cell data.☆14Jun 13, 2023Updated 2 years ago
- ☆17Jul 8, 2024Updated last year
- Fast, modular and reproducible generation of publication quality scientific figures and movies with only a few lines of code.☆17Apr 9, 2025Updated last year
- easy access to benchmark datasets☆50Aug 17, 2018Updated 7 years ago
- R package for computing Association Plots☆17Nov 4, 2024Updated last year
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Feb 19, 2026Updated 2 months ago
- GEfetch2R - Access Single-cell/Bulk RNA-seq Data from Public Repositories and Benchmark the Subsequent Format Conversion Tools☆40Mar 21, 2026Updated last month
- Scripts to install as a Bioconda package for making workflows☆18Sep 15, 2024Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Independent Component Analysis decipher functional modules for better cell clustering and annotation☆17Apr 4, 2022Updated 4 years ago
- An R package containing addins that are useful for Mine's workflow.☆26Nov 17, 2020Updated 5 years ago
- ☆39Aug 4, 2021Updated 4 years ago
- Paint genomes with taxa-specific k-mer probabilities☆15Apr 4, 2022Updated 4 years ago
- An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization☆19Aug 29, 2023Updated 2 years ago
- 6.790 | Machine Learning | Draft Site/Notes☆15Dec 5, 2025Updated 5 months ago
- List of papers on deconvolution of cell types in bulk RNA-seq based on single-cell signatures☆18Aug 28, 2020Updated 5 years ago
- Fast, accurate and scalable normalization for RNA sequencing data with the RUVprps software package.☆14Feb 23, 2026Updated 2 months ago
- Examples using Clustergrammer2 to explore high-dimensional datasets.☆40Aug 24, 2020Updated 5 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Cluster Identity Predictor (R package implementation)☆21Mar 8, 2022Updated 4 years ago
- Matrix factorization model for interpreting single cell gene expression in biologically heterogeneous data☆21Mar 25, 2024Updated 2 years ago
- Code for reproducing results from the paper "Modular and efficient pre-processing of single-cell RNA-seq data"☆23Feb 14, 2021Updated 5 years ago
- Rapid & standardized genome annotation using protein structural information☆63Updated this week
- Reconstruct the lineage topology of a scRNA-seq differentiation dataset.☆19Jun 25, 2020Updated 5 years ago
- Code for scKINETICS (ISMB 2023)☆22Oct 23, 2023Updated 2 years ago
- Run shell commands in a scientifically reproducible and robust way☆24Apr 23, 2026Updated 2 weeks ago