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datasets
datasets
 
 
.gitignore
.gitignore
 
 
10x_Genomics_Visium.R
10x_Genomics_Visium.R
 
 
2025scRNA_workflow.qmd
2025scRNA_workflow.qmd
 
 
ArchR.R
ArchR.R
 
 
BLM_six.qmd
BLM_six.qmd
 
 
DE_analysis_scrnaseq.Rmd
DE_analysis_scrnaseq.Rmd
 
 
GSE138794.qmd
GSE138794.qmd
 
 
GSE242889.qmd
GSE242889.qmd
 
 
GSVA.Rmd
GSVA.Rmd
 
 
Harmony.Rmd
Harmony.Rmd
 
 
Monocle3.R
Monocle3.R
 
 
README.Rmd
README.Rmd
 
 
README.md
README.md
 
 
SCENIC.Rmd
SCENIC.Rmd
 
 
ST_test.qmd
ST_test.qmd
 
 
Seurat4.Rmd
Seurat4.Rmd
 
 
Seurat5.qmd
Seurat5.qmd
 
 
Seurat_multimodal.R
Seurat_multimodal.R
 
 
Signnac.R
Signnac.R
 
 
SingleR.Rmd
SingleR.Rmd
 
 
SingleRV3.r
SingleRV3.r
 
 
Spatial_Transcripts.qmd
Spatial_Transcripts.qmd
 
 
TSCAN.Rmd
TSCAN.Rmd
 
 
cellChat.Rmd
cellChat.Rmd
 
 
cellphonedb.Rmd
cellphonedb.Rmd
 
 
cellranger.sh
cellranger.sh
 
 
check-all-markers.R
check-all-markers.R
 
 
fetching_annotations.R
fetching_annotations.R
 
 
follical_call_annotation.Rmd
follical_call_annotation.Rmd
 
 
get_KEGG.R
get_KEGG.R
 
 
heatmap_with_enrichment.R
heatmap_with_enrichment.R
 
 
heatmap_with_enrichment2.R
heatmap_with_enrichment2.R
 
 
inferCNV.Rmd
inferCNV.Rmd
 
 
inmmune_cells.qmd
inmmune_cells.qmd
 
 
liver_cancer.qmd
liver_cancer.qmd
 
 
mofa2.qmd
mofa2.qmd
 
 
monocle3.Rmd
monocle3.Rmd
 
 
monocle_lingang.qmd
monocle_lingang.qmd
 
 
scRNA-seq_from_tingting.R
scRNA-seq_from_tingting.R
 
 
scRNA_Analysis.qmd
scRNA_Analysis.qmd
 
 
scRNA_Notes.Rmd
scRNA_Notes.Rmd
 
 
scRepertoire.R
scRepertoire.R
 
 
seurat.R
seurat.R
 
 
single_cell_RNA.R
single_cell_RNA.R
 
 
single_cell_RNA.Rproj
single_cell_RNA.Rproj
 
 
spacexr_STalign.qmd
spacexr_STalign.qmd
 
 
tcell_markers_list.R
tcell_markers_list.R
 
 
velocyto.Rmd
velocyto.Rmd
 
 
临港实验室.qmd
临港实验室.qmd
 
 

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single_cell_RNA

The goal of single_cell_RNA is to record notes about scRNA-Seq analysis, this notes will update as i has more practice on scRNA-Seq.

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one by one steps for scRNA analysis. Just for take notes.

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single-cell

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