scToolbox

scToolbox is a collection of Matlab tools for analysis of single-cell sequencing type data.

Name		Name	Last commit message	Last commit date
Latest commit History 475 Commits
R		R
.gitignore		.gitignore
CellType.m		CellType.m
CellViewer.m		CellViewer.m
DEtest2.m		DEtest2.m
DEtestPairwise.m		DEtestPairwise.m
DEtestPairwiseAnova.m		DEtestPairwiseAnova.m
EnrichPlot.m		EnrichPlot.m
FindRpath.m		FindRpath.m
GO0000278_mitoticcellcycle.txt		GO0000278_mitoticcellcycle.txt
GOSemSim.R		GOSemSim.R
GOSemSim.m		GOSemSim.m
GOtrim.m		GOtrim.m
GroupedExpressionSummary.m		GroupedExpressionSummary.m
HGNC_hemoglobin_genes.txt		HGNC_hemoglobin_genes.txt
MNN_UMAP_Clust.m		MNN_UMAP_Clust.m
PDB_processed.mat		PDB_processed.mat
PanglaoDB_markers_27_Mar_2020.txt		PanglaoDB_markers_27_Mar_2020.txt
ReadMe.md		ReadMe.md
ScDataset.m		ScDataset.m
TODO.txt		TODO.txt
addGeneDatatips.m		addGeneDatatips.m
bimodality_coefficient.m		bimodality_coefficient.m
boxcox.m		boxcox.m
build_cluster_tree.m		build_cluster_tree.m
build_fig.m		build_fig.m
build_sparse_matrix.m		build_sparse_matrix.m
chi2test.m		chi2test.m
classify_cells.m		classify_cells.m
clustered_bubblechart.m		clustered_bubblechart.m
combat.m		combat.m
combat.py		combat.py
compareGeneLists.m		compareGeneLists.m
compile_summaries.m		compile_summaries.m
connectivityGraph.m		connectivityGraph.m
convertMTXtoH5.m		convertMTXtoH5.m
diffuse.m		diffuse.m
diptest.m		diptest.m
distinguishable_colors.m		distinguishable_colors.m
doClustering.m		doClustering.m
doDimRedAndCluster.m		doDimRedAndCluster.m
doPCA.m		doPCA.m
doPacMAP.m		doPacMAP.m
doTSNE.m		doTSNE.m
doUMAP.m		doUMAP.m
dotplot.m		dotplot.m
doubletDetection.m		doubletDetection.m
doubletDetection_old.m		doubletDetection_old.m
doubletFinder.R		doubletFinder.R
doublet_rates_10X.xlsx		doublet_rates_10X.xlsx
dscatter.m		dscatter.m
effectsizeContrasts.m		effectsizeContrasts.m
emptyDrops.m		emptyDrops.m
eulerr.R		eulerr.R
eulerr.m		eulerr.m
fast_pca.m		fast_pca.m
filterCellsAndGenes.m		filterCellsAndGenes.m
findGeneMoleculeOutliers.m		findGeneMoleculeOutliers.m
findMitoPerType.m		findMitoPerType.m
findSignificantPCs.m		findSignificantPCs.m
findVariableGenes.m		findVariableGenes.m
find_multimodal.m		find_multimodal.m
find_outliers.m		find_outliers.m
geneThresholdOtsu.m		geneThresholdOtsu.m
gene_tfidf.m		gene_tfidf.m
geneset_similarities.m		geneset_similarities.m
getExpression.m		getExpression.m
getExternalPath.m		getExternalPath.m
getGeneIndices.m		getGeneIndices.m
getMeanExpressionPerType.m		getMeanExpressionPerType.m
getPrctExpressionPerType.m		getPrctExpressionPerType.m
get_RGD_rat_genes.m		get_RGD_rat_genes.m
get_exclusive_intersections.m		get_exclusive_intersections.m
ggalluvial.R		ggalluvial.R
ggalluvial.m		ggalluvial.m
go_enrich_plot.m		go_enrich_plot.m
goatools.m		goatools.m
gprof_convert.m		gprof_convert.m
gprof_gost.m		gprof_gost.m
gprof_orth.m		gprof_orth.m
graph2idx.m		graph2idx.m
groupCountMatrix.m		groupCountMatrix.m
heatmap_plot.m		heatmap_plot.m
housekeepers_human.txt		housekeepers_human.txt
housekeepers_human_rat.csv		housekeepers_human_rat.csv
housekeepers_rat.txt		housekeepers_rat.txt
identifyDominantGenes.m		identifyDominantGenes.m
identifyDominantGenes_old.m		identifyDominantGenes_old.m
imputeCellType.m		imputeCellType.m
interp_cmap.m		interp_cmap.m
is_outlier.m		is_outlier.m
iterativeBinaryClassify.m		iterativeBinaryClassify.m
iterativeGroupClassify.m		iterativeGroupClassify.m
iterative_Otsu_classifier.m		iterative_Otsu_classifier.m
iterative_cdf_classifier.m		iterative_cdf_classifier.m
iterative_corr_classifier.m		iterative_corr_classifier.m
knnGraph.m		knnGraph.m
knn_metacells.m		knn_metacells.m
labelpoints.m		labelpoints.m
lasso.m		lasso.m

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