Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).
☆13Jan 12, 2024Updated 2 years ago
Alternatives and similar repositories for singleCellHaystack-py
Users that are interested in singleCellHaystack-py are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆11Sep 17, 2020Updated 5 years ago
- The analysis pipeline for FLEP-seq☆17Aug 18, 2023Updated 2 years ago
- Consistent Clusters for scRNA-seq☆11Oct 6, 2021Updated 4 years ago
- Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…☆57Jun 2, 2026Updated 2 months ago
- Comparison of single-cell normalization methods using multiple datasets with ground-truth labels☆19Dec 2, 2019Updated 6 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Single Cell Consensus Clustering with Speed☆24Dec 12, 2022Updated 3 years ago
- Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).☆92Dec 4, 2025Updated 8 months ago
- Correlation-Based Feature Selection for Single-Cell RNA Sequencing Data☆22Jul 19, 2022Updated 4 years ago
- Deposited codes for snMultiome in human cortex manuscript☆14Aug 12, 2024Updated last year
- This repository contains the code for reproducing all the results and figures from the preprint "Isoform specificity in the mouse primary…☆16Jul 16, 2021Updated 5 years ago
- Heterogeneity Induced Pre-Processing tOol☆19Aug 15, 2021Updated 4 years ago
- A set of files to do genomics analysis on python☆19Jun 5, 2025Updated last year
- Monet: An open-source Python package for analyzing scRNA-Seq data using PCA-based latent spaces☆41Sep 17, 2021Updated 4 years ago
- SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.☆97May 9, 2026Updated 3 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Web application demonstrating 3D modeling of spatial transcriptomics☆24Dec 9, 2024Updated last year
- Spatial Single Cell transcriptomic library☆22Jan 15, 2026Updated 6 months ago
- ☆19May 30, 2022Updated 4 years ago
- .h5mu files interface for Seurat☆34Nov 28, 2023Updated 2 years ago
- Single Cell Epigenome-based Inference of Activity☆19Sep 27, 2023Updated 2 years ago
- Python package for integrating and analyzing multiple single-cell datasets (A Python version of LIGER)☆31May 16, 2025Updated last year
- Python implementation of Monocle☆37Aug 21, 2025Updated 11 months ago
- a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.☆70Jul 9, 2026Updated last month
- Cookiecutter for community-maintained Jupyter Docker images☆18Aug 3, 2026Updated last week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Python package to perform normalization and variance-stabilization of single-cell data☆28Jul 17, 2025Updated last year
- Create cisTarget databases☆61Jun 18, 2025Updated last year
- Information-based dimensionality reduction☆30Dec 14, 2024Updated last year
- Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. It is recommended to use the raw spliced and unpliced cou…☆20Sep 29, 2025Updated 10 months ago
- ☆32Apr 12, 2023Updated 3 years ago
- MACA: Marker-based automatic cell-type annotation for single cell expression data☆25Jul 12, 2023Updated 3 years ago
- CELLEX (CELL-type EXpression-specificity)☆45Apr 29, 2026Updated 3 months ago
- FalseColor Python is a rapid digital staining module designed for translating two-channel fluorescence images (i.e. a nuclear and cytopla…☆34May 3, 2021Updated 5 years ago
- The scripts used for analyzing JAX mouse dataset☆26Oct 24, 2024Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- The first computational tool that enables both unsupervised and supervised discovery of tissue spatial domains☆34Jun 21, 2026Updated last month
- A flexible and fast sgRNA counter from FASTQ Files☆11Jun 17, 2026Updated last month
- Scalable Ultra-Sparse Bayesian PCA☆32Feb 13, 2024Updated 2 years ago
- The official implementation for "SANGO".☆11Mar 17, 2024Updated 2 years ago
- LIANA+: an all-in-one framework for cell-cell communication☆310Jul 16, 2026Updated 3 weeks ago
- A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing☆191Jun 9, 2026Updated 2 months ago
- Deep learning based processing of Atac-seq data☆137Feb 16, 2023Updated 3 years ago