R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
☆48Apr 8, 2022Updated 4 years ago
Alternatives and similar repositories for SCopeLoomR
Users that are interested in SCopeLoomR are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Guided construction of single cell reference☆12Jul 3, 2023Updated 2 years ago
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆481Apr 5, 2024Updated 2 years ago
- ☆12Nov 7, 2022Updated 3 years ago
- AUCell: score single cells with gene regulatory networks☆190Mar 9, 2024Updated 2 years ago
- A repository of pipelines for single-cell data in Nextflow DSL2☆81Apr 19, 2023Updated 2 years ago
- 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.
- Single Cell RNA-seq UMI Filtering Facilitator☆10Oct 6, 2025Updated 6 months ago
- R package for single cell and other data analysis using diffusion maps☆97Nov 9, 2025Updated 5 months ago
- Scripts needed to generate the figures for the Monocle 2 paper (Qiu et al, 2017)☆29Jul 1, 2020Updated 5 years ago
- Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs☆11Dec 21, 2019Updated 6 years ago
- Methods for visualization and analysis of spatially-resolved gene expression☆23Mar 19, 2026Updated 3 weeks ago
- Repo for website and other code for mouse sci-ATAC-seq project☆30Oct 1, 2020Updated 5 years ago
- Fast visualization tool for large-scale and high dimensional single-cell data☆78Dec 16, 2025Updated 3 months ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆633Updated this week
- scripts for analyzing data of macrophage development in human☆10Dec 8, 2019Updated 6 years ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Mapping out the coarse-grained connectivity structures of complex manifolds.☆238May 23, 2020Updated 5 years ago
- RNA velocity estimation in R☆196Sep 14, 2023Updated 2 years ago
- Blastocyst-like structures generated from human pluripotent stem cells☆13Sep 25, 2022Updated 3 years ago
- Code for EpiMap data browser☆14Jun 4, 2024Updated last year
- Automated cell type classification☆116Jan 3, 2025Updated last year
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆594Jun 26, 2025Updated 9 months ago
- ☆30Jul 15, 2021Updated 4 years ago
- ☆23Jan 20, 2021Updated 5 years ago
- Efficient and precise single-cell reference atlas mapping with Symphony☆115Oct 31, 2025Updated 5 months ago
- 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.
- Cell type purification by single-cell transcriptome-trained sorting☆14Jul 8, 2019Updated 6 years ago
- ☆444Jan 8, 2026Updated 3 months ago
- ☆63Jul 6, 2021Updated 4 years ago
- ☆23Nov 11, 2024Updated last year
- A short tutorial to using DL and keras for genomics with sequence data.☆15Dec 3, 2020Updated 5 years ago
- This repository contains HCA Benchmarking codes☆26Nov 11, 2019Updated 6 years ago
- Gene set variation analysis☆237Updated this week
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆319Nov 1, 2022Updated 3 years ago
- Simplify functional enrichment results☆124Jan 30, 2026Updated 2 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- chromatin Variability Across Regions (of the genome!)☆187Jul 10, 2024Updated last year
- Code used for mouse single cell RNAseq testis atlas☆12Nov 28, 2020Updated 5 years ago
- Community-provided extensions to Seurat☆359Feb 17, 2026Updated last month
- Hierarchical classification of cells☆28Aug 2, 2024Updated last year
- ☆33Apr 2, 2026Updated last week
- scRNA-seq workshop in Oxford on 9 September 2016☆11Sep 7, 2016Updated 9 years ago
- Repository for supplemental material of manuscripts☆19Jun 30, 2021Updated 4 years ago