Output Handling

annotate_cat	Generate colors and ids for categorical annotations
annotate_factor	Generate colors and ids for categorical annotations that are...
annotate_num	Generate colors and ids for numeric annotations
auto_annotate	Automatically format an annotation file
build_feather	Write scrattch data to feather files
check_tome_existence	Check if an object in a tome file exists
cl_to_anno	Convert a cl factor object to an annotation data.frame
collapse_along	Cumulatively collapse along a vector
create_desc	Create a generic description file
feather_to_list	Read a feather directory to a list of data.frames
flip_table	Transpose a gene x sample data.frame without losing a...
get_feather_data	Read data from a directory of feather files
group_annotations	Group annotation columns
jagged_to_data.frame	Convert a jagged list of gene counts to a data.frame
jagged_to_dgCMatrix	Convert a jagged list of gene counts to a sparse, dgCMatrix
jagged_to_matrix	Convert a jagged list of gene counts to a matrix
large_matrix_to_dgCMatrix	Convert a large matrix object to a dgCMatrix
read_10x_dgCMatrix	Read a whole sparse matrix directly from a 10X-style .h5 file
read_gene_data_hdf5	Read Gene Expression Data from an HDF5 file
read_h5ad_dgCMatrix	Read a whole sparse matrix directly from a .h5ad file
read_loom_anno	Read Loom sample annotations
read_loom_dgCMatrix	Read a Loom matrix as a dgCMatrix
read_loom_projections	Read Loom projections
read_shelf_gene_data	Read gene data across a set of tomes that share the same...
read_shelf_sample_data	Read sample data across a set of tomes that share the same...
read_tome_anno	Read annotations table from a tome file
read_tome_anno_desc	Read annotation descriptions table from a tome file
read_tome_data_dims	Get dims for data stored in a tome file.
read_tome_data.frame	Read a data.frame from a tome file
read_tome_dend	Read dendrogram object from a tome file
read_tome_dend_desc	Read dendrogram descriptions table from a tome file
read_tome_dgCMatrix	Read a whole sparse matrix directly from a tome file
read_tome_exon_lengths	Get exon lengths from a tome file
read_tome_gene_data	Read Gene Expression Data from a tome file
read_tome_gene_meta	Read gene metadata table from a tome file
read_tome_gene_meta_desc	Read gene metadata descriptions table from a tome file
read_tome_gene_names	Get all gene names in a tome file
read_tome_genes_jagged	Read tome gene count data as a jagged list
read_tome_intron_lengths	Get intron lengths from a tome file
read_tome_mapping	Read mapping table from a tome file
read_tome_mapping_desc	Read mapping descriptions table from a tome file
read_tome_projection	Read projection coordinates table from a tome file
read_tome_projection_desc	Read projection descriptions table from a tome file
read_tome_sample_data	Read Sample Expression Data from a tome file
read_tome_sample_names	Get all sample names in a tome file
read_tome_samples_jagged	Read tome sample count data as a jagged list
read_tome_serialized	Read a serialized object from a tome file
read_tome_stats	Read stats table from a tome file
read_tome_stats_desc	Read stats descriptions table from a tome file
read_tome_total_counts	Get total per-gene counts from a tome-file.
read_tome_vector	Read a vector from a tome (or other HDF5 object)
save_sparse_matrix_h5	Save a dgCMatrix to HDF5 format
set_scrattch.io_global_overwrite	Set global overwrite parameter
set_scrattch.io_global_verbosity	Set global verbosity parameter
values_to_colors	Convert values to colors along a color ramp
varibow	Generate a rainbow palette with variation in saturation and...
write_dgCMatrix_csv	Write a dgCMatrix to CSV in reasonable chunks
write_dgCMatrix_h5	Write a dgCMatrix to an h5 file similar to cellRanger format
write_tome_anno	Write an annotations table to a tome file.
write_tome_anno_desc	Write annotation desc table to a tome file.
write_tome_data	Save a both exon and intron counts to an HDF5 file (tome)
write_tome_data.frame	Generalized write for data.frames to a tome file
write_tome_dend	Write a dendrogram object as serialized ASCII to a tome file.
write_tome_dend_desc	Write a dend descriptions table to a tome file.
write_tome_dgCMatrix	Generalized write for dgCMatrix objects to a tome file
write_tome_exon_lengths	Write exon lengths to a tome file.
write_tome_gene_meta	Write gene info table to a tome file.
write_tome_gene_meta_desc	Write a gene metadata descriptions table to a tome file.
write_tome_group	Generate a new group in a tome file
write_tome_intron_lengths	Write intron lengths to a tome file.
write_tome_mapping	Write a mapping frequencies table to a tome file.
write_tome_projection	Write projection coordinates (e.g. tSNE or PCA) to a tome...
write_tome_projection_desc	Write a projection descriptions table to a tome file.
write_tome_serialized	Generalized write for individual serialized objects to a tome...
write_tome_sifter_stats	Caculate default stats for sifter and then write to tome
write_tome_stats	Write a stats table (e.g. median expression per cluster) to a...
write_tome_stats_desc	Write a stats descriptions table to a tome file.
write_tome_vector	Generalized write for individual vector objects to a tome...