This website hosts R Markdown reproducible notebooks for the bulk RNA-seq and the single-cell RNA-seq data analyses steps for the paper “Transcriptional reprogramming of skeletal muscle stem cells by the niche environment”.

The bioRxiv preprint of the paper can be accessed here.

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Scripts and Code

GitHub Link to Alevin QC Reports Folder

• Alevin QC reports for the seven scRNAseq samples.

Reproducible scRNA-seq Analysis Notebooks

1. Loading data.
2. Filtering cells.
3. Clustering cells.
4. Clustering celltypes.
5. Mark genes.
6. Running Differential expression analysis on stem cells.
7. Running Differential expression analysis on FAP cells.
8. Running Differential expression analysis on macrophage cells.
9. Plotting gene expression of stem cell markers.

Reproducible Bulk RNA-seq Analysis Notebooks

1. Analysis of pseudoaligned reads.
2. Combining bulk RNAseq and scRNAseq data.
3. Plotting gene expression.

ATACseq Workflow Reports

1. ATACseq worflow report for aged samples.
2. ATACseq worflow report for young samples.

Manuscript Revision Analyses

1. Dirichlet Regression to determine the effect of aging on cell-type composition in FACS data.
2. Comparison to Tabula Muris data .
3. Analysis of pseudoaligned reads (two batches).

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