https://github.com/bihealth/fracture-healing-and-aging-scseq
single-cell bone healing project
https://github.com/bihealth/fracture-healing-and-aging-scseq
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: ncbi.nlm.nih.gov, frontiersin.org, zenodo.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (9.1%) to scientific vocabulary
Repository
single-cell bone healing project
Basic Info
- Host: GitHub
- Owner: bihealth
- Language: R
- Default Branch: main
- Size: 66.3 MB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Project description
The scripts for Tchouto et. al paper on pronounced B cell impairment in adult immune-experienced mice link to article.
Data source
The data used in this repository were provided by the following contributors from the Julius Wolff Institute of Biomechanics and Musculoskeletal Regeneration:
- Dr. Christian H. Bucher
- Ann-Kathrin Mess
- Dr. Katharina Schmidt-Bleek
Contacts and links
- P.I: Georg Duda, Dieter Beule
- CUBI Contact: [Miha Milek] [mailto:milek@bih-charite.de]
Quick Start
For the preprocessing
- Download the FASTQ files from GEO (data owned by Dr. Christian H. Bucher): GSE273792.
- Run under Preprocessing: cellranger
- Run under Pre-processing: the single cell pipeline
For the processing:
Run the scripts under the processing folder to correct for any batch effects and integrate the data
Figures in the publication
The Seurat object used to reproduce the figures—based on data owned by Dr. Christian H. Bucher—can be downloaded from "zenodo link":
- git clone "repo"
- cd
.../Figures - Add the downloaded seurat objet to the folder
Figures/data. To install all the packages that are useful for creating the figures, use the already created environments inFigures/envs - run
Figures/Scripts/fig1.rmd ... Figures/Scripts/fig5.rmdto generate figure 2-6 and supplemental figures of the maunscript. Input data for the figures are found in the folderFigures/dataexcept for fig1a which is inFigures/images/fig1a.svg
Owner
- Name: Berlin Institute of Health
- Login: bihealth
- Kind: organization
- Website: https://www.cubi.bihealth.org/
- Repositories: 215
- Profile: https://github.com/bihealth
BIH Core Unit Bioinformatics & BIH HPC IT
GitHub Events
Total
- Push event: 1
- Public event: 1
Last Year
- Push event: 1
- Public event: 1