Cell marker identification and evaluation pipeline in single cell transcriptomes.
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Updated
Dec 18, 2024 - Jupyter Notebook
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marker-gene-identification
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Recreation and enrichment of the gastric (GC) cancer single-cell RNA-seq (scRNA-seq) data analysis pipeline described in the "Comprehensive analysis of metastatic gastric cancer tumour cells using single‑cell RNA‑seq" by Wang B. et. al, using the raw counts matrix they provide.
python machine-learning bioinformatics clustering pca tsne umap spectral-clustering single-cell-rna-seq louvain-algorithm ward-linkage sc-rna-seq go-annotation scanpy gmm-clustering sc-rna-seq-analysis average-linkage leiden-algorithm gastric-cancer marker-gene-identification
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Nov 25, 2024 - Jupyter Notebook
This repository contains code to analyze single-nuclei RNA sequencing data from the ventrobasal thalamus and principal sensory trigeminal nucleus in neonatal mice. It performs quality control, clustering, and identification of marker genes to characterize cell types and their interconnectivity during early whisker pathway development.
reproducibility single-cell-rna-sequencing-analysis neuronal-connectivity-and-development quality-control-filtering-single-nuclei graph-based-clustering-leiden-algorithm marker-gene-identification cell-type-characterization developmental-neuroscience whisker-system-somatosensory-pathway neuronal-connectivity-development
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Updated
Jan 19, 2024 - R
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