Files in ressy/srahelper
SRA Helper
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/biosamples.R
R/commands.R
R/constants.R
R/seqdata.R
R/sra_metadata.R
R/sra_submission.R
R/srahelper.R
R/tables.R
R/templates.R
README.md
inst/extdata/biosample_package_attributes.xml
inst/extdata/biosample_packages.xml
inst/extdata/templates/biosample_attributes/Beta-lactamase.1.0.tsv
inst/extdata/templates/biosample_attributes/Generic.1.0.tsv
inst/extdata/templates/biosample_attributes/Human.1.0.tsv
inst/extdata/templates/biosample_attributes/Invertebrate.1.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.air.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.built.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.host-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.human-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.human-gut.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.human-oral.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.human-skin.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.human-vaginal.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.microbial.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.miscellaneous.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.plant-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.sediment.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.soil.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.wastewater.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.ba.water.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.air.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.built.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.host-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.human-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.human-gut.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.human-oral.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.human-skin.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.human-vaginal.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.microbial.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.miscellaneous.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.plant-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.sediment.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.soil.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.wastewater.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.eu.water.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.air.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.built.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.host-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.human-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.human-gut.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.human-oral.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.human-skin.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.human-vaginal.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.microbial.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.miscellaneous.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.plant-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.sediment.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.soil.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.wastewater.4.0.tsv
inst/extdata/templates/biosample_attributes/MIGS.vi.water.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.air.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.built.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.host-associated.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.human-associated.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.human-gut.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.human-oral.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.human-skin.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.human-vaginal.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.microbial.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.miscellaneous.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.plant-associated.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.sediment.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.soil.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.wastewater.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMAG.water.5.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.air.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.built.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.host-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.human-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.human-gut.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.human-oral.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.human-skin.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.human-vaginal.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.microbial.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.miscellaneous.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.plant-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.sediment.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.soil.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.wastewater.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.specimen.water.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.air.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.built.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.host-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.human-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.human-gut.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.human-oral.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.human-skin.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.human-vaginal.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.microbial.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.miscellaneous.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.plant-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.sediment.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.soil.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.wastewater.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMARKS.survey.water.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.air.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.built.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.host-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.human-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.human-gut.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.human-oral.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.human-skin.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.human-vaginal.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.microbial.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.miscellaneous.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.plant-associated.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.sediment.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.soil.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.wastewater.4.0.tsv
inst/extdata/templates/biosample_attributes/MIMS.me.water.4.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.air.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.built.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.host-associated.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.human-associated.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.human-gut.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.human-oral.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.human-skin.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.human-vaginal.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.microbial.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.miscellaneous.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.plant-associated.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.sediment.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.soil.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.wastewater.5.0.tsv
inst/extdata/templates/biosample_attributes/MISAG.water.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.air.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.built.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.host-associated.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.human-associated.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.human-gut.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.human-oral.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.human-skin.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.human-vaginal.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.microbial.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.miscellaneous.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.plant-associated.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.sediment.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.soil.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.wastewater.5.0.tsv
inst/extdata/templates/biosample_attributes/MIUVIG.water.5.0.tsv
inst/extdata/templates/biosample_attributes/Metagenome.environmental.1.0.tsv
inst/extdata/templates/biosample_attributes/Microbe.1.0.tsv
inst/extdata/templates/biosample_attributes/Model.organism.animal.1.0.tsv
inst/extdata/templates/biosample_attributes/Pathogen.cl.1.0.tsv
inst/extdata/templates/biosample_attributes/Pathogen.env.1.0.tsv
inst/extdata/templates/biosample_attributes/Plant.1.0.tsv
inst/extdata/templates/biosample_attributes/Virus.1.0.tsv
inst/extdata/templates/library_metadata/SRA_metadata.tsv
man/BLANK_TYPES.Rd
man/FIXED_VOCABULARY.Rd
man/HTTP_SRV.Rd
man/biosamples.Rd
man/blank.Rd
man/build_biosamples_from_template.Rd
man/build_metadata.Rd
man/build_sra_submission.Rd
man/check_uniqueness.Rd
man/chunk_submission.Rd
man/datemunge.Rd
man/download_biosample_attributes.Rd
man/download_biosample_packages.Rd
man/download_metadata.Rd
man/download_template.Rd
man/dump_metadata.Rd
man/field_descriptions.Rd
man/fill_blanks.Rd
man/fill_from_columns.Rd
man/has_zero_seqs.Rd
man/list_template_types.Rd
man/list_templates.Rd
man/process_fixed_vocab.Rd
man/read_biosample_attributes.Rd
man/read_biosample_packages.Rd
man/read_template.Rd
man/seqdata.Rd
man/sra_metadata.Rd
man/sra_submission.Rd
man/srahelper-package.Rd
man/tables.Rd
man/templates.Rd
man/tidy_optional_fields.Rd
man/validate_fields.Rd
man/validate_sra_submission.Rd
man/write_biosamples.Rd
man/write_sra_submission.Rd
man/write_table.Rd
tests/testthat.R
tests/testthat/helpers.R
tests/testthat/test_biosamples.R
tests/testthat/test_seqdata.R
tests/testthat/test_sra_metadata.R
tests/testthat/test_sra_submission.R
tests/testthat/test_tables.R
tests/testthat/test_templates.R
