https://github.com/broadinstitute/dropsift
cell caller for sn/snRNA sequence data
Science Score: 36.0%
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
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✓Committers with academic emails
2 of 2 committers (100.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.6%) to scientific vocabulary
Repository
cell caller for sn/snRNA sequence data
Basic Info
- Host: GitHub
- Owner: broadinstitute
- License: other
- Language: R
- Default Branch: main
- Size: 17.7 MB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
DropSift
DropSift is a nucleus caller for single-nucleus RNA sequencing data.
This tool distinguishes between nuclei and empty droplets by combining summary metrics of cell barcodes—such as total UMI counts, fraction of intronic reads, and percentage of mitochondrial reads. It also incorporates gene expression to learn signatures characteristic of empty droplets, and can optionally make use of CellBender’s remove-background outputs. DropSift uses these features to robustly identify true nuclei across a variety of datasets.
Installation
To install the latest version directly from GitHub:
if (!require("remotes")) {
install.packages("remotes")
}
remotes::install_github("broadinstitute/DropSift")
Documentation
A complete guide—including input file formats, example usage, and a detailed walkthrough of the algorithmic steps—is available here
License
This package is released under the MIT License.
Owner
- Name: Broad Institute
- Login: broadinstitute
- Kind: organization
- Location: Cambridge, MA
- Website: http://www.broadinstitute.org/
- Twitter: broadinstitute
- Repositories: 1,083
- Profile: https://github.com/broadinstitute
Broad Institute of MIT and Harvard
GitHub Events
Total
- Issues event: 4
- Delete event: 16
- Issue comment event: 11
- Member event: 1
- Push event: 59
- Pull request event: 31
- Create event: 19
Last Year
- Issues event: 4
- Delete event: 16
- Issue comment event: 11
- Member event: 1
- Push event: 59
- Pull request event: 31
- Create event: 19
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Alec Wysoker | a****w@b****g | 21 |
| jamesnemesh | n****h@b****g | 5 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 2
- Total pull requests: 26
- Average time to close issues: 11 days
- Average time to close pull requests: about 12 hours
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 2.0
- Average comments per pull request: 0.31
- Merged pull requests: 22
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 26
- Average time to close issues: 11 days
- Average time to close pull requests: about 12 hours
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 2.0
- Average comments per pull request: 0.31
- Merged pull requests: 22
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jamesnemesh (2)
Pull Request Authors
- alecw (24)
- jamesnemesh (6)