Man pages for AlexsLemonade/scpcaTools
Single cell data tools for ScPCA
| add_cellhash_ids | Add cellhash sample information to altExperiment rowData |
| add_cell_mito_qc | Calculate QC metrics for all reads and mitochondrial subset... |
| add_demux_hashedDrops | Add cellhash demultiplexing results using... |
| add_demux_seurat | Add cellhash demultiplexing results using Seurat::HTODemux() |
| add_demux_vireo | Add genetic demultiplexing results to a SCE object from Vireo |
| add_gene_symbols | Add Gene symbols to a SingleCellExperiment from a GTF file |
| add_miQC | Add miQC model and probability compromised to a... |
| add_sample_metadata | Add data frame with sample metadata to an SCE object |
| build_sce | Build the SCE object from the counts matrix |
| calculate_ilisi | Calculate iLISI (integration Local Inverse Simpson's Index)... |
| calculate_silhouette_width | Calculate silhouette width scores from a merged SCE object. |
| calculate_within_batch_ari | Calculate within-batch ARI scores from a merged SCE object. |
| check_metadata | Helper function to check that expected metadata fields are... |
| cluster_sce | Perform clustering on a SingleCellExperiment object |
| coldata_to_df | Convert colData from SingleCellExperiment to a data.frame |
| collapse_intron_counts | Merge counts from intron reads with corresponding cDNA reads |
| downsample_pcs | Downsample PCs for use in integration metric calculations |
| filter_counts | Filter counts matrix using DropletUtils::emptyDropsCellRanger |
| filter_pcs | Remove cells with NA batch label from PCs and label rownames |
| generate_qc_report | Generate a QC report from a SingleCellExperiment object |
| get_altexp_attributes | Helper function to check altExp compatibility |
| get_altexp_metadata | Helper function to get altExp metadata from an SCE that may... |
| import_quant_data | Import Gene Expression Quantification Data for Single-Cell... |
| integrate_fastmnn | Integrate a list of SingleCellExperiment (SCE) objects using... |
| integrate_harmony | Integrate a list of SingleCellExperiment (SCE) objects using... |
| integrate_sces | Integrate a merged set of SingleCellExperiment objects using... |
| merge_altexp | Add an alternative experiment to a SingleCellExperiment by... |
| merge_sce_list | Merge a list of SCEs into one SCE object |
| metadata_to_coldata | Add sample metadata to colData of SCE object |
| miQC_nofilter | miQC_nofilter |
| prepare_altexp_for_merge | Prepare an alternative experiment for merging |
| prepare_merged_metadata | Prepare an updated list of metadata for the merged SCE |
| prepare_sce_for_merge | Helper function to prepare an SCE object for merging |
| read_alevin | Read in counts data processed with Alevin or Alevin-fry |
| read_cellranger | Read in counts data processed with Cell Ranger |
| read_kallisto | Read in counts data processed with Kallisto |
| read_tximport | Read in counts data processed with Alevin or alevin-fry in... |
| rowdata_to_df | Convert rowData from SingleCellExperiment to a data.frame |
| sce_to_anndata | Convert SingleCellExperiment objects to AnnData file stored... |
| sce_to_seurat | Convert SingleCellExperiment object to Seurat object |
| scpcaTools-package | scpcaTools: Useful tools for analysis of single-cell RNA seq... |
| silhouette_width_from_pcs | Calculate silhouette width scores using PCs from a merged SCE... |
| sim_sce | Create a random SingleCellExperiment object |
| within_batch_ari_from_pcs | Calculate within-batch ARI using provided PCs for use in... |
