Man pages for jacobheng/cellwrangler
Supplemental toolkit for single-cell RNAseq analysis

annotate_bcvCalculate and annotate biological coefficent of variation
calculate_mt_exprsCalculate mitochondrial gene expression
CellType_genes_jitterPlot gene expression for all CellTypes as jitter plots
create_monocle_cdsCreate a monocle CellDataSet object from a directory of...
createMultiSoupChannelCreate multiple Soup Channels from an cellranger-aggregated...
CreateSeuratObjectListCreate a list of Seurat Objects
createSoupChannelCreate a single Soup Channel
dim_coord_barcodeFind rownames of cells from coordinates of dimensionality...
emptySoupEstimate expression profile of soup from empty droplets
exprs_thresholdDetermine if cells are above an expression threshold of a...
find_CCA_genesFind high variance genes for CCA
findGeneIDFind Ensembl gene IDs given gene names
findGeneNameFind gene names given Ensembl gene IDs
find_highbcv_genesFind genes with high biological coefficent of variation
findRowsFind rows by row names
find_sample_dispersed_genesFind dispersed genes in each sample in CellDataSet
find_sample_expressed_genesFind expressed genes in each sample in CellDataSet
fit_cds_vglmFit vector generalized linear model to a CellDataSet object
gene_barplotPlot mean gene expression as bar plot
gene_jitterplotPlot expression of cells as jitter plot
get_kegg_databaseGet kegg database for an organism
get_kegg_pathway_genesGet genes for a kegg pathway
get_patternMarkerNamesGet pattern markers as gene names for a set of CoGAPS results
load_10X_matrixLoad an expression matrix from a directory of...
load_CoGAPS_resLoad a set of CoGAPS results
log_normalize_cdsNormalize and log monocle cds
make_rnkMake rank lists
merge_by_rownamesMerge dataframes or matrices by rownames
merge_df_listMerge a list of dataframes or matrices
plot_bcvPlot biological coefficent of variation and annotate genes
plot_CoGAPS_ChiSqPlots the mean ChiSq values of a set of CoGAPS results
plot_drops_diagnosticsPlot diagnostic plot for testDrops results
plot_gene_exprsPlot gene expression in cells
plot_groupsPlot cell groups
plot_matrix_dendrogramPlot a clustered dendrogram
plot_matrix_heatmapPlot a clustered heatmap
plot_mean_exprs_heatmapPlot mean expression heatmap
plot_pathway_dendrogramPlot pathway dendrogram
plot_pathway_heatmapPlot pathway heatmap
plot_pattern_cor_dendrogramPlot pattern correlation dendrogram
plot_pattern_cor_heatmapPlot pattern correlation heatmap
plot_pattern_dimPlot pattern on a dimensionality reduction plot
plot_patternSet_dimPlot a set of patterns on a dimensionality reduction plot
plot_pheatmapPlot pheatmap object
plot_sparse_pca_varPlot variance explained by sparse PCA
rowSDGet standard deviation for rows in a matrix
rowSEGet standard error of the mean for rows in a matrix
sparse_pca_biplotPlot biplot for sparse pca
spectral_tsneReduce dimensions of a matrix with pca and tSNE
spectral_umapReduce dimensions of a matrix with pca and UMAP
split_aggr_mtxSplit a cellranger-aggregated matrix into multiple matrices...
summarize_cds_exprsGet gene-level summary statistics for CellDataSet object
testDropsDetermine whether droplets are cells or blank drops in an...
jacobheng/cellwrangler documentation built on March 22, 2019, 2:39 a.m.