Man pages for scPipe
pipeline for single cell RNA-seq data analysis

anno_importImport gene annotation
anno_to_safConvert annotation from GenomicRanges to Simple Annotation...
calculate_QC_metricsCalcuate QC metrics from gene count matrix
cell_barcode_matchingcell barcode demultiplex statistics for a small sample...
convert_geneidconvert the gene ids of a SingleCellExperiment object
create_processed_reportcreate_processed_report
create_reportcreate_report
create_sce_by_dircreate a SingleCellExperiment object from data folder...
demultiplex_infodemultiplex_info
detect_outlierDetect outliers based on QC metrics
dot-qq_outliers_robustDetect outliers based on robust linear regression of QQ plot
gene_id_typeGet or set 'gene_id_type' from a SingleCellExperiment object
get_ercc_annoGet ERCC annotation table
get_genes_by_GOGet genes related to certain GO terms from biomart database
get_read_strGet read structure for particular scRNA-seq protocol
organismGet or set 'organism' from a SingleCellExperiment object
plot_demultiplexplot_demultiplex
plot_mappingPlot mapping statistics for 'SingleCellExperiment' object.
plot_QC_pairsPlot GGAlly pairs plot of QC statistics from...
plot_UMI_dupPlot UMI duplication frequency
QC_metricsGet or set quality control metrics in a SingleCellExperiment...
remove_outliersRemove outliers in 'SingleCellExperiment'
sc_count_aligned_bamsc_count_aligned_bam
sc_demultiplexsc_demultiplex
sc_demultiplex_and_countsc_demultiplex_and_count
sc_detect_bcsc_detect_bc
sc_exon_mappingsc_exon_mapping
sc_gene_countingsc_gene_counting
scPipescPipe - single cell RNA-seq pipeline
sc_sample_dataa small sample scRNA-seq counts dataset to demonstrate...
sc_sample_qcquality control information for a small sample scRNA-seq...
sc_trim_barcodesc_trim_barcode
UMI_dup_infoGet or set UMI duplication results in a SingleCellExperiment...
UMI_duplicationUMI duplication statistics for a small sample scRNA-seq...
scPipe documentation built on Oct. 31, 2019, 6:01 a.m.