GitHub - qinqian/rms_analysis: single cell data analysis for rms

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Name		Name	Last commit message	Last commit date
Latest commit History 33 Commits
annotation		annotation
drug		drug
larry		larry
larry_latest		larry_latest
larry_optimized		larry_optimized
lisa_script_modules		lisa_script_modules
revision1		revision1
20082_refine.R		20082_refine.R
Ahbinav_grants.R		Ahbinav_grants.R
DEGs_seurat3.R		DEGs_seurat3.R
DEGs_seurat3_sara.R		DEGs_seurat3_sara.R
EGFR_RD_RH41.r		EGFR_RD_RH41.r
Fig1.R		Fig1.R
Fig1_cell_proportion.R		Fig1_cell_proportion.R
Fig1_integration.R		Fig1_integration.R
Fig1_integration.ipynb		Fig1_integration.ipynb
Fig1_integration_cellassign.R		Fig1_integration_cellassign.R
Fig1_integration_recluster_individual_tumor.R		Fig1_integration_recluster_individual_tumor.R
Fig2.R		Fig2.R
Fig3.R		Fig3.R
Fig4.R		Fig4.R
Fig4.ipynb		Fig4.ipynb
Fig4_dynamical_latentime.ipynb		Fig4_dynamical_latentime.ipynb
Fig4_dynamical_latentime.py		Fig4_dynamical_latentime.py
Fig4_explore.R		Fig4_explore.R
Fig4_integrated_velocity.ipynb		Fig4_integrated_velocity.ipynb
Fig4_integrated_velocity.py		Fig4_integrated_velocity.py
Fig5.R		Fig5.R
Fig5_integration_1and10cells.R		Fig5_integration_1and10cells.R
Fig5_integration_muscle.R		Fig5_integration_muscle.R
Fig5_velocity.ipynb		Fig5_velocity.ipynb
MYC_MYCN_RMS.r		MYC_MYCN_RMS.r
RD_analyze.r		RD_analyze.r
Snakefile.10x		Snakefile.10x
Zebrafish2122recluster.r		Zebrafish2122recluster.r
analysis_seurat3_sara.R		analysis_seurat3_sara.R
annotate_celltypes.R		annotate_celltypes.R
annotate_celltypes_updated.R		annotate_celltypes_updated.R
annotate_primary_tumor.R		annotate_primary_tumor.R
cellranger.sh		cellranger.sh
check_seu_velocity.R		check_seu_velocity.R
claudia_emt_muscle_surface.r		claudia_emt_muscle_surface.r
compare_muscle_emt.r		compare_muscle_emt.r
corr_heatmap.R		corr_heatmap.R
cross_species.R		cross_species.R
doublet_ratio.r		doublet_ratio.r
download_basespace.sh		download_basespace.sh
dynamical_commands.sh		dynamical_commands.sh
functions.R		functions.R
generate_manual_gtf.py		generate_manual_gtf.py
generate_v4_degenes.R		generate_v4_degenes.R
generate_v6_degenes.R		generate_v6_degenes.R
gsea_pipeline.R		gsea_pipeline.R
identify_doublet.py		identify_doublet.py
infercnv.R		infercnv.R
integrate_all_samples.py		integrate_all_samples.py
intersect_seurat_velocity_toloom.R		intersect_seurat_velocity_toloom.R
lisa_gsea_multiple_plot.R		lisa_gsea_multiple_plot.R
lisa_gsea_multiple_plot_designfig.R		lisa_gsea_multiple_plot_designfig.R
lme_test.r		lme_test.r
mdfi_corr.R		mdfi_corr.R
merge_lisa_gene_set.R		merge_lisa_gene_set.R
multi_velocity_plot.R		multi_velocity_plot.R
niche_analysis.R		niche_analysis.R
nichenet.R		nichenet.R
output_cellstates.r		output_cellstates.r
phemd.r		phemd.r
plot.py		plot.py
plot_r01.r		plot_r01.r
plot_rd_mast139.r		plot_rd_mast139.r
primary_marker_visualize.R		primary_marker_visualize.R
recluster_velocity_excludingblood.R		recluster_velocity_excludingblood.R
row_normalized_heatmap.R		row_normalized_heatmap.R
run.sh		run.sh
run_genewalk.sh		run_genewalk.sh
run_include_primary.sh		run_include_primary.sh
run_monocle.sh		run_monocle.sh
scanpy_velocity_stream.ipynb		scanpy_velocity_stream.ipynb
seurat_genes.R		seurat_genes.R
seurat_monocle3.r		seurat_monocle3.r
seurat_monocle3_pipeline.r		seurat_monocle3_pipeline.r
seurat_monocle_velocity_pipe.R		seurat_monocle_velocity_pipe.R
seurat_pipeline.R		seurat_pipeline.R
seurat_sara_pipeline.R		seurat_sara_pipeline.R
seurat_to_loom.R		seurat_to_loom.R
seurat_velocity.R		seurat_velocity.R
stream_from_seurat_vel_monocle.ipynb		stream_from_seurat_vel_monocle.ipynb
stream_pipeline.py		stream_pipeline.py
test.py		test.py
test.sh		test.sh
test_plot.R		test_plot.R
upset.r		upset.r
velocity_heatmap.py		velocity_heatmap.py
velocity_pipeline.R		velocity_pipeline.R
velocity_pipeline.py		velocity_pipeline.py
velocity_pipeline_dynamical_latentime.py		velocity_pipeline_dynamical_latentime.py
velocity_pipeline_steady.py		velocity_pipeline_steady.py
velocity_r.sh		velocity_r.sh