https://github.com/brickmanlab/proks-et-al-2023
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
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✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (3.8%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: brickmanlab
- Language: Jupyter Notebook
- Default Branch: master
- Size: 11.5 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
proksetal_2023
Complemetary analysis to nf-core/marsseq.
Dataset available at 
nf-core/marsseq
```bash module load java/11.0.15 nextflow/22.10.6 singularity/3.8.0
sh nf-coretower.sh mm10ref nextflow run $PIPELINEPATH/nf-core-marsseq \ --input $DATAPATH/SB26/design.csv \ --buildreferences \ --genomesbase /scratch/Brickman/references \ --genome mm10
sh nf-coretower.sh SB26 nextflow run $PIPELINEPATH/nf-core-marsseq \ --input $DATAPATH/SB26/design.csv \ --genomesbase /scratch/Brickman/references \ --genome mm10
sh nf-coretower.sh SB28 nextflow run $PIPELINEPATHnf-core-marsseq \ --input $DATAPATH/SB28/design.csv \ --genomesbase /scratch/Brickman/references \ --genome mm10 ```
MARS-seq2.0
```bash module load miniconda/latest
source activate ngs cookiecutter https://github.com/brickmanlab/mars-seq2-inhouse
source activate mars python helpers/prepare.py --input $PIPELINEPATH/pipeline/SB26/ --output testdata
split cells per Batch
scripts/splitfastqs.sh testdata/rawreads/SB26/origfiles/ testdata/rawreads/SB26/ 4000000 scripts/splitfastqs.sh testdata/rawreads/SB28/origfiles/ testdata/rawreads/SB28/ 4000000
run pipeline
scripts/runpipelinelocally.sh test_data ```
Owner
- Name: Brickman group
- Login: brickmanlab
- Kind: organization
- Location: Copenhagen
- Website: https://danstem.ku.dk/research1/brickman/
- Repositories: 3
- Profile: https://github.com/brickmanlab
Professor Joshua Brickman at Center for Stem Cell Medicine (reNEW), University of Copenhagen
GitHub Events
Total
- Push event: 2
Last Year
- Push event: 2