A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.
☆51Jan 9, 2026Updated last month
Alternatives and similar repositories for spilterlize_integrate
Users that are interested in spilterlize_integrate are comparing it to the libraries listed below
Sorting:
- CeMM's Snakemake SLURM cluster profile☆47Oct 8, 2025Updated 4 months ago
- A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq re…☆52Dec 7, 2025Updated 2 months ago
- Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.☆96Nov 25, 2025Updated 3 months ago
- A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, p…☆72Sep 24, 2025Updated 5 months ago
- Workflow to Fetch Public Sequencing Data and Metadata Using iSeq and MrBiomics Module.☆42Jun 23, 2025Updated 8 months ago
- RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.☆41Aug 5, 2025Updated 7 months ago
- A toolkit for NGS analysis with Python☆14Jan 18, 2023Updated 3 years ago
- Accessible and interoperable whole slide image analysis☆185Feb 28, 2026Updated last week
- R Bindings for htslib/bcf☆10Oct 4, 2023Updated 2 years ago
- Single-cell Graph Cuts Optimization☆16Apr 27, 2024Updated last year
- A short tutorial to using DL and keras for genomics with sequence data.☆15Dec 3, 2020Updated 5 years ago
- Repository for "NucleoBench: A Large-Scale Benchmark of Neural Nucleic Acid Design Algorithms"☆26Nov 22, 2025Updated 3 months ago
- Deep learning models to predict enhancers in different Drosophila embryo tissues☆20Dec 10, 2023Updated 2 years ago
- ☆20Apr 7, 2025Updated 10 months ago
- Domain based annotation of transposable elements☆21Oct 8, 2025Updated 4 months ago
- Benchmark of GRNs using the GRETA pipeline☆31Feb 24, 2026Updated last week
- Network-based project to explore gene connectivity through biological scales☆23Oct 21, 2024Updated last year
- Image Mass Cytometry analysis pipeline☆26Jun 3, 2025Updated 9 months ago
- Pipeline for functional annotation of genomes by integrating data from RNA-seq, ChIP-seq, DNase-seq, etc.☆26Feb 23, 2022Updated 4 years ago
- ☆26Dec 25, 2023Updated 2 years ago
- A python implementation of spatial entropy☆25Dec 15, 2023Updated 2 years ago
- Legend made easy for matplotlib☆34Jun 7, 2025Updated 8 months ago
- 🔄 Hot module reload for python, automatically reload your code when files are modified. No need to modify source code.☆33Nov 20, 2025Updated 3 months ago
- A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.☆32Jan 3, 2023Updated 3 years ago
- GPU-accelerated Stain Normalization and Augmentation in PyTorch☆40Feb 10, 2026Updated 3 weeks ago
- A Snakemake executor plugin for submitting jobs to a SLURM cluster☆48Feb 26, 2026Updated last week
- Project metadata manager for PEPs in Python☆40Jan 5, 2026Updated 2 months ago
- inferring regulatory cellular dynamics☆64Jan 13, 2026Updated last month
- CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…☆57Feb 20, 2026Updated 2 weeks ago
- scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics☆58Aug 17, 2024Updated last year
- OTGNN code☆56Jun 5, 2020Updated 5 years ago
- Computational Optimization of DNA Activity (CODA)☆67Apr 3, 2025Updated 11 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆76Nov 2, 2025Updated 4 months ago
- spatial transcriptome, single cell☆73Mar 18, 2023Updated 2 years ago
- Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.☆97Nov 13, 2025Updated 3 months ago
- Creating figures and animations for multi-channel images with a focus on microscopy.☆80Dec 16, 2024Updated last year
- A Python toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.☆106Feb 11, 2026Updated 3 weeks ago
- A Python-based compendium of GPU-optimized aging clocks.☆121Feb 18, 2026Updated 2 weeks ago
- Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.☆81Jan 20, 2026Updated last month