scMerge
Statistical approach for removing unwanted variation from multiple single-cell datasets
Science Score: 23.0%
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✓DOI references
Found 8 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
4 of 11 committers (36.4%) from academic institutions -
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Low similarity (14.0%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Statistical approach for removing unwanted variation from multiple single-cell datasets
Basic Info
- Host: GitHub
- Owner: SydneyBioX
- Language: R
- Default Branch: master
- Homepage: https://sydneybiox.github.io/scMerge/
- Size: 128 MB
Statistics
- Stars: 67
- Watchers: 10
- Forks: 13
- Open Issues: 5
- Releases: 2
Topics
Metadata Files
README.md
scMerge
scMerge is a R package for merging and normalising single-cell RNA-Seq
datasets.
Installation
scMerge is available on Bioconductor
(https://bioconductor.org/packages/scMerge). You can install it using:
``` r
Install scMerge from Bioconductor, requires R 3.6.0 or above
BiocManager::install("scMerge")
You can also try to install the Bioconductor devel version of scMerge:
BiocManager::install("scMerge", version = "devel") ```
Vignette
You can find the vignette at our website:
- scMerge: https://sydneybiox.github.io/scMerge/articles/scMerge.html.
- scMerge2: https://sydneybiox.github.io/scMerge/articles/scMerge2.html.
Stably Expressed Genes
Stably expressed genes identified from this study can be extracted by
library(scMerge)
data(segList)
segList$human$human_scSEG # human SEG
segList$mouse$mouse_scSEG # mouse SEG
Or download csv files here (human SEG: link; mouse SEG: link)
For more detailed information and evaluation about SEG, please see our publication https://doi.org/10.1093/gigascience/giz106.
Contact us
If you have any enquiries, especially about performing scMerge
integration on your own data, then please contact
yingxin.lin@sydney.edu.au. You can also open an
issue on GitHub.
Reference
scMerge: scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets. Yingxin Lin, Shila Ghazanfar, Kevin Y.X. Wang, Johann A. Gagnon-Bartsch, Kitty K. Lo, Xianbin Su, Ze-Guang Han, John T. Ormerod, Terence P. Speed, Pengyi Yang, Jean Y. H. Yang. (2019). Our manuscript published at PNAS can be found here.
scMerge2: Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2. Yingxin Lin, Yue Cao, Elijah Willie, Ellis Patrick, Jean Y.H. Yang. (2023). Our manuscript published in Nature Communications can be found here.
Owner
- Name: Sydney Precision Data Science Centre
- Login: SydneyBioX
- Kind: organization
- Location: Sydney, Australia
- Website: https://www.sydney.edu.au/science/our-research/research-centres/sydney-precision-data-science-centre.html
- Twitter: sydneybioinfo
- Repositories: 76
- Profile: https://github.com/SydneyBioX
SPDSC alliance brings together multiple research groups and junior and senior researchers with shared interests in bioinformatics and computational sciences.
GitHub Events
Total
- Watch event: 2
- Fork event: 1
Last Year
- Watch event: 2
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| kevinwang09 | k****g@s****u | 198 |
| yingxinlin | y****y@g****m | 44 |
| Nitesh Turaga | n****a@g****m | 14 |
| Kevin Wang GCP | k****9@g****m | 3 |
| Mark Greenaway | m****g@m****u | 2 |
| kevinwang | k****9 | 2 |
| J Wokaty | j****y@s****u | 2 |
| Hervé Pagès | h****s@f****g | 1 |
| Yingxin Lin | y****n@p****u | 1 |
| Darío Hereñú | m****a@g****m | 1 |
| Yingxin Lin | 3****n | 1 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
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Total downloads:
- bioconductor 35,198 total
- Total dependent packages: 2
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: scMerge
scMerge: Merging multiple batches of scRNA-seq data
- Homepage: https://github.com/SydneyBioX/scMerge
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/scMerge/inst/doc/scMerge.pdf
- License: GPL-3
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Latest release: 1.24.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/upload-artifact v3 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/upload-artifact v3 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- actions/cache v1 composite
- actions/checkout v3 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- R >= 3.6.0 depends
- BiocNeighbors * imports
- BiocParallel * imports
- BiocSingular * imports
- DelayedArray * imports
- DelayedMatrixStats * imports
- M3Drop >= 1.9.4 imports
- S4Vectors >= 0.23.19 imports
- SingleCellExperiment >= 1.7.3 imports
- SummarizedExperiment * imports
- batchelor * imports
- cluster * imports
- cvTools * imports
- distr * imports
- igraph * imports
- methods * imports
- proxyC * imports
- ruv * imports
- scater * imports
- scran * imports
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