https://github.com/ahmedmoustafa/cerebellum-atlas-analysis
Code and scripts used in analysis of snRNAseq cerebellar cortex atlas
Science Score: 23.0%
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Code and scripts used in analysis of snRNAseq cerebellar cortex atlas
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Fork of MacoskoLab/cerebellum-atlas-analysis
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https://github.com/ahmedmoustafa/cerebellum-atlas-analysis/blob/master/
# cerebellum-atlas-analysis Code and scripts used in analysis of snRNAseq mouse cerebellum atlas, as described in our recent [preprint](https://www.biorxiv.org/content/10.1101/2020.03.04.976407v1.abstract). Example scripts used for clustering and cell type annotation are available in `annotation`. ## Figures Markdown files to reproduce the main figures are available in `main_figures` and below: [Figure 1: Cerebellar cell type annotation](https://raw.githack.com/MacoskoLab/cerebellum-atlas-analysis/master/main_figures/cb_figure1.html) [Figure 2: Characterization of spatial variation](https://raw.githack.com/MacoskoLab/cerebellum-atlas-analysis/master/main_figures/cb_figure2.html) [Figure 3: Cross-cluster continuity of neuronal populations](https://raw.githack.com/MacoskoLab/cerebellum-atlas-analysis/master/main_figures/cb_figure3.html) [Figure 4: Characterization of MLI2 cells](https://raw.githack.com/MacoskoLab/cerebellum-atlas-analysis/master/main_figures/cb_figure4.html) [Figure 4: Development of MLI2 cells](https://raw.githack.com/MacoskoLab/cerebellum-atlas-analysis/master/main_figures/cb_figure4_DE.html) Some custom functions for Seurat/LIGER object manipulation and analysis (not yet available in LIGER) are included in `cb_custom_functions.R` and `src`. ## Data Processed count matrices can be downloaded from [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165371) and [Single Cell Portal](https://singlecell.broadinstitute.org/single_cell/study/SCP795). Additional metadata and smFISH data are available in `data`.
Owner
- Name: Ahmed Moustafa
- Login: ahmedmoustafa
- Kind: user
- Location: Egypt
- Company: American University in Cairo
- Website: https://ahmedmoustafa.com/
- Repositories: 12
- Profile: https://github.com/ahmedmoustafa
Bioinformatics and Genomics Data Scientist