https://github.com/bioconductor/tenxbrainanalysis
R scripts for analyzing the 1.3 million brain cell data set from 10X Genomics
Science Score: 23.0%
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○CITATION.cff file
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○.zenodo.json file
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2 of 4 committers (50.0%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (5.9%) to scientific vocabulary
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Repository
R scripts for analyzing the 1.3 million brain cell data set from 10X Genomics
Basic Info
- Host: GitHub
- Owner: Bioconductor
- Language: R
- Default Branch: devel
- Size: 37.1 KB
Statistics
- Stars: 12
- Watchers: 6
- Forks: 2
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Scripts for analyzing the 10X 1.3 million brain cell data
The scripts should be executed in the following order:
intro.Rmd: An introduction, duh.preprocess.Rmd: Downloading the data and quality controlcycle.Rmd: Cell cycle phase assignmentnormalize.Rmd: Calculation of cell-specific size factorsvariance.Rmd: Identification of highly variable genesdimred.Rmd: Dimensionality reduction with randomized PCA
Various output objects will be saved to objects/.
A few of these objects are currently hosted at https://drive.google.com/open?id=10WbmJ2BriLKlyKEf1Bbb8K0NwD9rw-.
Note that sce.rds does not contain the actual counts or normalized expression values, and requires something like this:
r
library(TENxBrainData)
tenx <- TENxBrainData()
sce <- readRDS("sce.rds")
tenx <- tenx[,colnames(sce)] # drop 19,672 cells from the raw TENxBrainData
counts(sce) <- counts(tenx) # overwrite inbuilt absolute path
library(scater)
sce <- normalize(sce) # generate normalized expression values
The pics/make_pics.R scripts will generate the figures used in the paper.
Owner
- Name: Bioconductor
- Login: Bioconductor
- Kind: organization
- Website: https://bioconductor.org
- Repositories: 156
- Profile: https://github.com/Bioconductor
Software for the analysis and comprehension of high-throughput genomic data
GitHub Events
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Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Aaron Lun | a****n@w****u | 33 |
| LTLA | a****n@c****k | 9 |
| Kevin Rue-Albrecht | k****7@g****m | 1 |
| Charlotte Soneson | c****n@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 1
- Total pull requests: 1
- Average time to close issues: 29 minutes
- Average time to close pull requests: 1 minute
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 2.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- mdozmorov (1)
Pull Request Authors
- kevinrue (1)