Man pages for denalitherapeutics/archs4
Wrappers to query and extract ARCHS4 data
| archs4_feature_info | Retrieves the feature (gene/transcript) information for the... |
| archs4_file_info | Retrieves a table of files that back an Archs4Repository |
| archs4_file_path | Identify the file path on the system for specific ARCHS4... |
| archs4_local_data_dir_create | Initialize a local datadir to act as an ARCHS4 data datadir |
| archs4_local_data_dir_validate | Check "the health" of a local ARCHS4 data datadir |
| archs4_meta | Retrieves the meta information associated with an ARCHS4... |
| Archs4Repository | An interface to a locally downloaded ARCHS4 dataset |
| archs4_sample_covariates | Retrieves tibble of sample-level covariates available in... |
| archs4_sample_info | Retrieves information for samples by GSE series or sample IDs |
| archs4_sample_table | Lists the GEO series and samples available in the human and... |
| archs4_series_status | Checks which samples from a single series are present/absent. |
| archs4_sources | Lists the different sources ARCHS4 is built for |
| as.DGEList | Create a DGEList for the expression data of a series or set... |
| blacklist | Return a list of series/samples you may want to ignore for... |
| create_augmented_feature_info | Create meta information for the genes and transcripts in the... |
| datadir | Retrieves the directory that contains the data for the... |
| dot-h5read | Read data from an HDF5 file "with caution" |
| estimate_norm_factors | Calculates library size and norm factors for a specific... |
| estimate_repository_norm_factors | Estimate normalization factors for datasets in the... |
| feature_lookup | Perform a loose/fuzzy lookup for a gene/transcript feature. |
| feature_source | Retrieves (organism) source of gene/transcript identifiers |
| fetch_expression | Retrieve expression data for genes/transcripts across samples |
| geo_id_type | Classify a vector of sample or series GEO ID's as such |
| libstats | Extract the read depth and normalization factors for the... |
| lookup_biosamples | Retrieve sample annotations from NCBI's Biosample database |
| lookup_gse | Retrieve information about a GEO series |
| query_geo | Query NCBI GEO through its REST interface |
| retrieve_sra_metadata | Retrieve metadata for an SRA accession |
