Man pages for ressy/srahelper
SRA Helper

biosamplesNCBI BioSamples
blankCheck for blank cells
BLANK_TYPESBioSample empty field values
build_biosamples_from_templateCreate BioSamples Table
build_metadataCreate blank metadata
build_sra_submissionCreate BioSamples Attributes and SRA Metadata Tables
check_uniquenessCheck sample uniqueness from metadata
chunk_submissionChunk up submission data frames
datemungeConvert date text strings into YYY-MM-DD
download_biosample_attributesDownload BioSample Attributes XML
download_biosample_packagesDownload BioSample Package info XML
download_metadataDownload Library Metadata Template
download_templateDownload BioSample Template
dump_metadataDownload BioSample Metadata
field_descriptionsGet BioSample field descriptions
fill_blanksFill blanks with NCBI-allowed keyword
fill_from_columnsFill in columns from reference
FIXED_VOCABULARYMetadata fields with restricted values
has_zero_seqsReport files containing no sequences
HTTP_SRVNCBI server hostnames
list_templatesList installed template files
list_template_typesList template types
process_fixed_vocabCreate factors for known fields with fixed vocabulary
read_biosample_attributesRead BioSample attributes list from file
read_biosample_packagesRead BioSample package information from file
read_templateRead table template
seqdataSequence Data Functions
srahelper-packageSRA Helper
sra_metadataNCBI SRA Metadata
sra_submissionNCBI SRA Submissions
tablesNCBI Metadata Tables
templatesNCBI Submission Templates
tidy_optional_fieldsRemove blank optional fields
validate_fieldsCheck metadata fields for problems
validate_sra_submissionCheck both SRA submission spreadsheets for problems
write_biosamplesWrite BioSample attributes or metadata to disk
write_sra_submissionWrite SRA submission spreadsheets to disk
write_tableRead and write metadata to disk
ressy/srahelper documentation built on May 29, 2019, 11:03 p.m.