Files in rezakj/scSeqR
scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.
.DS_Store
DESCRIPTION
NAMESPACE
R/add.adt.R
R/add.vdj.R
R/adt.rna.merge.R
R/cell.filter.R
R/cell.gating.R
R/change.clust.R
R/clust.avg.exp.R
R/clust.cond.info.R
R/clust.rm.R
R/clust.stats.plot.R
R/cluster.plot.R
R/data.aggregation.R
R/data.scale.R
R/diff.exp.R
R/down.sample.R
R/find.dim.genes.R
R/findMarkers.R
R/gate.to.clust.R
R/gene.plot.R
R/gene.stats.R
R/heatmap.gg.plot.R
R/heatmap.plot.R
R/imm.gen.R
R/load10x.R
R/lvbsc.R
R/make.gene.model.R
R/make.obj.R
R/make.scseqr.obj.R
R/man.assign.clust.R
R/myclass.R
R/norm.adt.R
R/norm.data.R
R/opt.clust.num.R
R/opt.pcs.plot.R
R/prep.vdj.R
R/pseudotime.tree.R
R/qc.stats.R
R/run.clustering.R
R/run.diff.st.R
R/run.diffusion.map.R
R/run.magic.R
R/run.pc.tsne.R
R/run.pca.R
R/run.tsne.R
R/run.umap.R
R/stats.plot.R
R/top.markers.R
R/tsne.plot.R
R/volcano.ma.plot.R
README.md
build/vignette.rds
data/datalist
data/g2m.phase.rda
data/immgen.rna.rda
data/immgen.uli.rna.rda
data/myHTOS.png
data/s.phase.rda
doc/12_pseudotime.png
doc/13_monocol.png
doc/14_monocol.png
doc/19_clonotypes.png
doc/1_AllClusts.png
doc/2_AllConds.png
doc/3_clust_cond_freq_info_bar.png
doc/4_clust_cond_freq_info_pie.png
doc/5_cluster_gene_cov.png
doc/6_cluster_mito_ratio.png
doc/7_cluster_KEGGpathways.png
doc/7_genePlots.png
doc/8_genePlots.png
doc/9_heatmap_gg.png
doc/Anchor.png
doc/CV.pdf
doc/Compare.png
doc/Conds.png
doc/Conds_clusts.gif
doc/Diffusion.png
doc/ImmGen_for_Cluster_4.png
doc/ImmGen_for_Cluster_7.png
doc/ImmGen_heatmap_RNA_Cluster_1.png
doc/ImmGen_heatmap_RNA_Cluster_2.png
doc/ImmGen_heatmap_RNA_Cluster_3.png
doc/ImmGen_heatmap_RNA_Cluster_4.png
doc/ImmGen_heatmap_RNA_Cluster_5.png
doc/ImmGen_heatmap_RNA_Cluster_6.png
doc/ImmGen_heatmap_RNA_Cluster_7.png
doc/ImmGen_heatmap_ULI-RNA_Cluster_7.png
doc/ImmGen_pointPlot_RNA_Cluster_1.png
doc/ImmGen_pointPlot_RNA_Cluster_2.png
doc/ImmGen_pointPlot_RNA_Cluster_3.png
doc/ImmGen_pointPlot_RNA_Cluster_4.png
doc/ImmGen_pointPlot_RNA_Cluster_5.png
doc/ImmGen_pointPlot_RNA_Cluster_6.png
doc/ImmGen_pointPlot_RNA_Cluster_7.png
doc/ImmGen_pointPlot_ULI-RNA_Cluster_7.png
doc/ImmGen_pointPlot_for_Cluster_4.png
doc/ImmGen_pointPlot_for_Cluster_7.png
doc/MA_plot.html
doc/MA_plot.png
doc/MNN.png
doc/MS4A1_PCA.png
doc/MS4A1_bar.png
doc/MS4A1_box.png
doc/MS4A1_tSNE.png
doc/NotScaled.png
doc/Opt_Number_Of_PCs.png
doc/PCA_conds.png
doc/PCA_density.png
doc/Slide1.png
doc/Slide1_1.png
doc/Slide2.png
doc/Slide3.png
doc/Slide5.png
doc/Slide5_1.png
doc/Slide8.png
doc/TCGA.png
doc/UMAP.png
doc/UMAP_2D.png
doc/UMAP_2D_clusters.html
doc/UMAP_MS4A1.png
doc/Workflow_scSeqR.jpg
doc/aCCCA.png
doc/aCPCA.png
doc/aMNN.png
doc/aS1.png
doc/aS3.png
doc/aSeurat.png
doc/bar.png
doc/bloodCells.jpg
doc/box.gene.clusters.png
doc/box.mito.clusters.png
doc/cellGating.txt
doc/clust_cond_freq_info.txt
doc/density_clusters.png
doc/density_conditions.png
doc/diffiusion3D.gif
doc/dst.png
doc/dst_2D.png
doc/dst_IL7R.png
doc/dst_plot.html
doc/f.gif
doc/first.gif
doc/gate1.png
doc/gate2.png
doc/gate3.png
doc/gating2.gif
doc/gene-umi-plot.html
doc/gene.model.html
doc/gene.model.png
doc/gene.umi.png
doc/heatmap.html
doc/heatmap.png
doc/heatmap_Cluster_7.png
doc/heatmaps.png
doc/iCellR_1.png
doc/imputed_BoxPlot.png
doc/imputed_dotPlot.png
doc/imputed_heatmap.png
doc/list1.png
doc/list3.png
doc/list5.png
doc/logo.png
doc/mito-umi-plot.html
doc/mito.umi.png
doc/optim_clust_num1.png
doc/out.gif
doc/out1.gif
doc/out10.gif
doc/out2.gif
doc/out3.gif
doc/out4.gif
doc/out5.gif
doc/out6.gif
doc/pie.png
doc/pseudotime.tree_cladogram.png
doc/pseudotime.tree_classic.png
doc/pseudotime.tree_fan.png
doc/pseudotime.tree_jitter.png
doc/pseudotime.tree_radial.png
doc/pseudotime.tree_unrooted.png
doc/pseudotime.tree_unrooted2.png
doc/scSeqR-workflow.jpg
doc/scSeqR-workflow.png
doc/stats.png
doc/stats2.png
doc/tSNE_2D_a.png
doc/tSNE_2D_b.png
doc/tSNE_2D_c.png
doc/tSNE_2D_clusters.html
doc/tSNE_2D_clusters.png
doc/tSNE_2D_d.png
doc/tSNE_2D_e.png
doc/tSNE_2D_f.png
doc/tSNE_3D.png
doc/tSNE_3D_clusters.html
doc/tSNE_conds.png
doc/tSNE_conds_density.png
doc/tSNE_density.png
doc/uli_RNA_metadat.txt
doc/umap-learn.png
doc/umap-naive.png
doc/vdj.stats.png
doc/volc_plot.html
doc/volc_plot.png
doc/workflow.jpg
doc/workflow.png
inst/doc/introduction.R
inst/doc/introduction.Rmd
inst/doc/introduction.html
man/add.adt.Rd
man/add.vdj.Rd
man/adt.rna.merge.Rd
man/cell.filter.Rd
man/cell.gating.Rd
man/change.clust.Rd
man/clust.avg.exp.Rd
man/clust.cond.info.Rd
man/clust.rm.Rd
man/clust.stats.plot.Rd
man/cluster.plot.Rd
man/data.aggregation.Rd
man/data.scale.Rd
man/diff.exp.Rd
man/down.sample.Rd
man/find.dim.genes.Rd
man/findMarkers.Rd
man/gate.to.clust.Rd
man/gene.plot.Rd
man/gene.stats.Rd
man/heatmap.gg.plot.Rd
man/heatmap.plot.Rd
man/imm.gen.Rd
man/load10x.Rd
man/lvbsc.Rd
man/make.gene.model.Rd
man/make.obj.Rd
man/make.scseqr.obj.Rd
man/man.assign.clust.Rd
man/norm.adt.Rd
man/norm.data.Rd
man/opt.clust.num.Rd
man/opt.pcs.plot.Rd
man/prep.vdj.Rd
man/pseudotime.tree.Rd
man/qc.stats.Rd
man/run.clustering.Rd
man/run.diff.st.Rd
man/run.diffusion.map.Rd
man/run.magic.Rd
man/run.pc.tsne.Rd
man/run.pca.Rd
man/run.tsne.Rd
man/run.umap.Rd
man/stats.plot.Rd
man/top.markers.Rd
man/tsne.plot.Rd
man/volcano.ma.plot.Rd
vignettes/figure/unnamed-chunk-1-1.png
vignettes/figure/unnamed-chunk-1-2.png
vignettes/introduction.Rmd
vignettes/introduction.md
