numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
Science Score: 46.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: nature.com -
✓Committers with academic emails
5 of 10 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.4%) to scientific vocabulary
Keywords
Repository
Haplotype-aware CNV analysis from single-cell RNA-seq
Basic Info
- Host: GitHub
- Owner: kharchenkolab
- License: other
- Language: R
- Default Branch: main
- Homepage: https://kharchenkolab.github.io/numbat/
- Size: 390 MB
Statistics
- Stars: 191
- Watchers: 8
- Forks: 25
- Open Issues: 79
- Releases: 0
Topics
Metadata Files
README.md
Numbat
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Numbat is a haplotype-aware CNV caller from single-cell and spatial transcriptomics data. It integrates signals from gene expression, allelic ratio, and population-derived haplotype information to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship.
Numbat can be used to: 1. Detect allele-specific copy number variations from scRNA-seq and spatial transcriptomics 2. Differentiate tumor versus normal cells in the tumor microenvironment 3. Infer the clonal architecture and evolutionary history of profiled tumors.
Numbat does not require paired DNA or genotype data and operates solely on the donor scRNA-seq data (for example, 10x Cell Ranger output). For details of the method, please checkout our paper:
User Guide
For a complete guide, please see Numbat User Guide.
Questions?
We appreciate your feedback! Please raise a github issue for bugs, questions and new feature requests. For bug reports, please attach full log, error message, input parameters, and ideally a reproducible example (if possible).
Owner
- Name: Kharchenko Lab
- Login: kharchenkolab
- Kind: organization
- Website: http://pklab.org
- Twitter: KharchenkoLab
- Repositories: 21
- Profile: https://github.com/kharchenkolab
GitHub Events
Total
- Issues event: 35
- Watch event: 25
- Issue comment event: 38
- Push event: 31
- Pull request review comment event: 9
- Pull request review event: 9
- Pull request event: 8
- Fork event: 3
Last Year
- Issues event: 35
- Watch event: 25
- Issue comment event: 38
- Push event: 31
- Pull request review comment event: 9
- Pull request review event: 9
- Pull request event: 8
- Fork event: 3
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| teng-gao | g****g@w****u | 411 |
| teng-gao | t****g@g****m | 256 |
| evanbiederstedt | e****t@g****m | 81 |
| Teng Gao | t****o@g****u | 24 |
| hiraksarkar | h****r@u****u | 10 |
| evanbiederstedt | e****t | 3 |
| Teng Gao | t****o@a****u | 2 |
| whtns | k****k@g****m | 2 |
| Stefanos Alexandros Bamopoulos | s****m@h****g | 1 |
| igor | 6****t | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 199
- Total pull requests: 18
- Average time to close issues: about 2 months
- Average time to close pull requests: 3 days
- Total issue authors: 113
- Total pull request authors: 5
- Average comments per issue: 2.61
- Average comments per pull request: 2.89
- Merged pull requests: 16
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 25
- Pull requests: 8
- Average time to close issues: 14 days
- Average time to close pull requests: about 20 hours
- Issue authors: 21
- Pull request authors: 1
- Average comments per issue: 0.8
- Average comments per pull request: 0.0
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- teng-gao (17)
- aelhossiny (6)
- aranham (6)
- kokonech (5)
- DarioS (5)
- stela2502 (4)
- Summerhythm (4)
- ccruizm (3)
- wangsky137 (3)
- MigleMi (3)
- cathalgking (3)
- laijen000 (3)
- rosaranli (3)
- petrsh (3)
- thomasveith (3)
Pull Request Authors
- lijin0303 (7)
- evanbiederstedt (5)
- igordot (2)
- whtns (2)
- sbamopoulos (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- cran 434 last-month
- Total docker downloads: 90
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 16
- Total maintainers: 1
proxy.golang.org: github.com/kharchenkolab/numbat
- Documentation: https://pkg.go.dev/github.com/kharchenkolab/numbat#section-documentation
- License: other
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Latest release: v1.4.2
published over 1 year ago
Rankings
cran.r-project.org: numbat
Haplotype-Aware CNV Analysis from scRNA-Seq
- Homepage: https://github.com/kharchenkolab/numbat/
- Documentation: http://cran.r-project.org/web/packages/numbat/numbat.pdf
- License: MIT + file LICENSE
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Latest release: 1.4.2
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.0.0 depends
- GenomicRanges * imports
- IRanges * imports
- Matrix * imports
- R.utils * imports
- Rcpp * imports
- RcppParallel * imports
- RhpcBLASctl * imports
- Rsamtools * imports
- VGAM * imports
- ape * imports
- argparse * imports
- caTools * imports
- data.table * imports
- dendextend * imports
- dplyr * imports
- extraDistr * imports
- ggplot2 * imports
- ggraph * imports
- ggtree * imports
- glue * imports
- gtools * imports
- igraph * imports
- logger * imports
- magrittr * imports
- parallel * imports
- parallelDist * imports
- patchwork * imports
- phangorn * imports
- pryr * imports
- purrr * imports
- reshape2 * imports
- roptim * imports
- stringr * imports
- tidygraph * imports
- tidyr * imports
- vcfR * imports
- zoo * imports
- matrixStats * suggests
- testthat >= 3.0.0 suggests