Man pages for AllenInstitute/BarMixer
Hashed scRNA-seq demultiplexing for .h5 files
| add_cell_ids | Add cell IDs to a h5_list object |
| add_h5_list_hash_results | Add cell hashing results to an h5_list. |
| add_h5_transposed_matrix | Add a transposed version of a matrix to an .h5 file |
| add_missing_hto_rows | Add zero values for missing HTOs to a matrix |
| add_well_metadata | Add well metadata |
| binarize_hash | Binarize a vector of hash counts based on a cutoff value |
| binarize_hash_matrix | Binarize a matrix of hash counts |
| categorize_binary_hash_matrix | Convert binary hash matrix results to categorical labels for... |
| cat_h5_list | Concatenate two h5_list objects. |
| check_matrix | Simple function to check for matrix or dgCMatrix classes for... |
| choose_chunk_size | Select a reasonable chunk size for an HDF5 dataset object |
| choose_integer_bits | Decide how many bits to use to store integer values in an... |
| convert_char_na | Convert "NA" character entries to actual NAs |
| convert_char_na_recursive | Convert all "NA" character values to actual NAs recursively |
| get_list_path | Retrieve an object from a list using path-style targeting |
| h5_attr_list | Generate a set of attributes based on 10x Genomics defaults |
| h5dims | Get dimensions of an object in an HDF5 file |
| h5dump | Dump all objects from an HDF5 file to a list. |
| h5exists | Check if an object exists in an HDF5 file |
| h5_list_add_dgCMatrix | Add a sparse matrix to an h5_list containing 10x genomics... |
| h5_list_add_mito_umis | Add mitochondrial gene UMI counts to an h5_list object |
| h5_list_cell_metadata | Extract a data.frame of cell metadata from an h5_list object |
| h5_list_convert_from_dgCMatrix | Convert the matrix in an h5_list from a sparse matrix back to... |
| h5_list_convert_to_dgCMatrix | Convert the matrix in an h5_list from 10x Genomics data to a... |
| h5_list_transpose | Transpose an h5_list object |
| h5ls | List objects in an HDF5 file |
| hello | Hello, World! |
| is_unimodal | Test if a hash distribution is unimodal |
| make_singlet_summary | Generate a summary table with the number and fraction of... |
| qc_aligned_barplot | Generate a baseline-aligned barplot for two categorical... |
| qc_cutoff_barplot | Generate a QC Barplot for a metric at multiple cutoffs |
| qc_flip | Flip the orientation of a data.frame and return as a list. |
| qc_frac_hist_plot | Generate a QC Histogram Plot for a single fractional metric |
| qc_hist_plot | Generate a QC Histogram Plot for a single metric |
| qc_scatter_plot | Generate a QC Scatter Plot for a pair of metrics |
| qc_stacked_barplot | Generate a stacked barplot for two categorical metrics |
| qc_table | Render a nicely-formatted table for QC reports |
| qc_violin_plot | Generate a QC Violin Plot for a metric, grouped by a... |
| read_csc_mtx | Read a CITE-seq-Count .mtx directory as a standard R matrix |
| read_h5_cell_meta | Read .h5 Cell Metadata |
| read_h5_dgCMatrix | Read the /matrix from a .h5 file as a sparse matrix |
| read_h5_feature_meta | Read .h5 Feature Metadata |
| read_h5_sce | Read .h5 directly into a SingleCellExperiment object |
| read_h5_seurat | Read .h5 directly into a Seurat Object |
| read_tenx_metrics | Read and correct formatting of a 10x metrics_summary.csv file |
| reduce_h5_list | Reduce a list-of-lists of h5_list objects to a single,... |
| select_hash_cutoff | Select a cutoff for hash counts using automatic, k-means... |
| set_list_path | Set a list value using path-style targeting |
| split_h5_list_by_hash | Split a 10x HDF5 file based on HTOparser results |
| stm | Write a stderr message with a leading date/time stamp |
| strip_1d_array_recursive | Convert all 1D Arrays in a list object to vectors recursively |
| subset_h5_list_by_observations | Subset a h5_list object based on a set of observations. |
| totalseq_a_biotin | Load BioLegend TotalSeq A reference table for biotin hash tag... |
| totalseq_a_human | Load BioLegend TotalSeq A reference table for human hash tag... |
| totalseq_a_mouse | Load BioLegend TotalSeq A reference table for mouse hash tag... |
| varibow | Generate a rainbow palette with variation in saturation and... |
| write_h5_list | Write an h5_list, as created by rhdf5::h5dump(), to an .h5... |
