Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separately or in combination). Allele-specific estimation allows for the more accurate delineation of copy number states and the detection of subclonal copy-neutral loss-of-heterozygosity and mirrored CNA events. On…
☆32Mar 10, 2023Updated 3 years ago
Alternatives and similar repositories for Alleloscope
Users that are interested in Alleloscope are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Inferring CNV data from single cell ATAC seq☆28Jun 24, 2025Updated last year
- Clonalscope is a subclone detection method based on copy number alterations (CNAs) for single-cell and ST tumor sequencing data. Clonalsc…☆32Sep 30, 2025Updated 9 months ago
- R package to detect breakpoints and assign somies to scATAC-seq data☆43Dec 1, 2025Updated 7 months ago
- CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links☆44Nov 13, 2024Updated last year
- CONICS: COpy-Number analysis In single-Cell RNA-Sequencing☆77Feb 27, 2023Updated 3 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.☆23Jun 10, 2025Updated last year
- A tool for detecting somatic variants in single cell data☆224Sep 15, 2024Updated last year
- Implementation of FACETS for Terra☆12Jan 20, 2023Updated 3 years ago
- Toolkit for single-cell copy number analysis☆35Dec 15, 2025Updated 7 months ago
- Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines☆47Mar 13, 2025Updated last year
- Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome☆223Feb 4, 2026Updated 5 months ago
- DNAscan2 is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring v…☆14May 7, 2024Updated 2 years ago
- ☆298Jun 16, 2026Updated last month
- A computational method for inferring the cancer cell fraction of tumour structural variation from whole-genome sequencing data.☆44Aug 21, 2025Updated 11 months 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.
- Trajectory Inference Based on SNP information.☆24Jun 19, 2024Updated 2 years ago
- Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"☆22May 11, 2018Updated 8 years ago
- Genomic plot in trellis layout☆43Jan 30, 2026Updated 5 months ago
- XEnograft Visualization & Analysis☆11Oct 18, 2025Updated 9 months ago
- Machine learning use cases for teaching☆13Jul 12, 2017Updated 9 years ago
- Tools for single-cell data processing☆136May 27, 2024Updated 2 years ago
- mitochondrial variant analysis tools☆15Mar 4, 2021Updated 5 years ago
- Map single-cell transcriptomes to copy number evolutionary trees.☆14Aug 18, 2024Updated last year
- Signature Analysis and Visualization for Single-Cell RNA-seq☆182Jun 10, 2024Updated 2 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.
- Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.☆38Apr 13, 2026Updated 3 months ago
- Single-cell Bisulfite Sequencing Data Mapping☆13May 19, 2021Updated 5 years ago
- ☆14Nov 2, 2017Updated 8 years ago
- An R Bioconductor package providing interactive connections to igv.js (the Integrative Genomics Viewer) in a web browser☆46May 1, 2026Updated 2 months ago
- Generate the UMI count matrix from CEL-Seq2 sequencing data☆19Oct 12, 2018Updated 7 years ago
- Notebook and examples related to La Manno and Gyllborg et al. 2016☆17Mar 4, 2017Updated 9 years ago
- Classify output of AmpliconArchitect to detect types of focal amplifications present☆23Updated this week
- ☆91Apr 5, 2021Updated 5 years ago
- ☆35Jul 8, 2025Updated last year
- 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.
- SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data☆42Jul 6, 2023Updated 3 years ago
- ☆59Mar 18, 2026Updated 4 months ago
- Metacell - Single-cell mRNA Analysis☆121Updated this week
- Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks☆30Updated this week
- A set of Pyro models and functions to infer CNA from scRNA-seq data☆11Aug 14, 2023Updated 2 years ago
- Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis☆21Mar 15, 2023Updated 3 years ago
- scripts to automatically update ANNOVAR db☆19Nov 17, 2021Updated 4 years ago