Method Name

Description

add_cell_ids

Add cell IDS to a h5_list object

add_h5_list_adt_results

Add ADT results to an h5_list

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_well_metadata

Add well metadata

append_ext_h5_character

Append character values to an existing HDF5 string dataset

cat_h5_list

Concatenate two h5_list objects

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 HDF5 Dataset object

convert_char_na

Convert “NA” character entries to actual NAs

convert_char_na_recursive

Convert all NA character values to actual NAs recursively

create_ext_h5_character

Create an extensible character HDF5 dataset

create_ext_h5_float

Create an extensible float HDF5 dataset

create_ext_h5_uint

Create an extensible unsigned integer HDF5 dataset

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

h5_list_add_dgCMatrix

Add a sparse matrix to an h5_list containing 10x Genomics data

h5_list_add_mita_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 its original structure

h5_list_convert_to_dgCMatrix

Convert the matrix in an h5_list from 10x Genomics data to a sparse matrix

h5_list_transpose

Transpose an h5_list object

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

h5ls

List objects in an HDF5 file

qc_aligned_barplot

Generate a baseline-aligned barplot for two categorical metrics

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_stacked_barplot

Generate a stacked barplot for two categorical metrics

qc_table

Render a nicole formatted table for QC metrics

qc_violin_plot

Generate a QC violin plot for a metric, grouped by a categorical metadata column

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 .h5ad feature metadata

read_tenx_metrics

Read and correct formatting of a 10x metics_summary.csv file

reduce_h5_list

Reduce a list-of-lists of h5_list objects to a single, concatenated object

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 data/time stamp

strip_1d_array_recursive

Convert all 1D arrays in a list object to vector recursively

subset_h5_list_by_observations

Subset a h5_list object based on a set of observations

varibow

Generate a rainbow palette with variation in saturation and value

write_10x_h5_container

Generate an empty HDF5 container to store RNA-seq count data in 10x format

write_h5_list

Write an h5_list, as created by rhddf5::h5dump(), to an .h5 file