Files in bhklab/AnnotationGx
AnnotationGx: A package for building, updating and querying an annotation database for pharmaco-genomic data
.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/issue_template.md
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.gitignore
AnnotationGx.code-workspace
DESCRIPTION
Dockerfile
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/AnnotationGx-data.R
R/AnnotationGx-package.R
R/CancerTargetDiscovery.R
R/GuideToPharm.R
R/biomart_core.R
R/cellosaurus.R
R/cellosaurus_annotations.R
R/cellosaurus_helpers.R
R/chembl.R
R/chembl_helpers.R
R/oncotree.R
R/pubchem_helpers.R
R/pubchem_rest.R
R/pubchem_status.R
R/pubchem_view.R
R/pubchem_view_helpers.R
R/unichem.R
R/unichem_helpers.R
R/utils-general.R
R/utils-httr2.R
R/utils-logging.R
R/utils-matchNested.R
R/utils-split.R
R/utils-standardize_names.R
README.md
_pkgdown.yml
data-raw/CCLE/CCLE_sampleMetadata.R
data-raw/CCLE/CCLE_treatmentdata.R
data-raw/CTRP/CTRP_sampleMetadata.R
data-raw/CTRP/CTRP_treatmentMetadata.R
data-raw/GDSC/GDSC_sampleMetadata.R
data-raw/GDSC/GDSC_treatmentMetadata.R
data-raw/gCSI/gCSI_sampleMetadata.R
data-raw/gCSI/gCSI_treatmentMetadata.R
data-raw/old/cell_model_passports_models.R
data-raw/sample_pipeline.Rmd
data-raw/treatment_pipeline.Rmd
data/CCLE_sampleMetadata.rda
data/CCLE_treatmentMetadata.rda
data/CTRP_sampleMetadata.rda
data/CTRP_treatmentMetadata.rda
data/GDSC_sampleMetadata.rda
data/GDSC_treatmentMetadata.rda
data/gCSI_sampleMetadata.rda
data/gCSI_treatmentMetadata.rda
inst/extdata/CCLE/CCLE_Cell_lines_annotations_20181226.txt
inst/extdata/CCLE/CCLE_NP24.2009_profiling_2012.02.20.csv
inst/extdata/CTRP/CTRPv2_meta_per_cell_line.txt
inst/extdata/CTRP/v20.meta.per_compound.txt
inst/extdata/CellModelPassports/cell_model_passports_list_20240103.csv
inst/extdata/Cell_Lines_Details.xlsx
inst/extdata/GDSC/GDSC2_8.4_treatmentMetadata.csv
inst/extdata/GDSC/GDSC_8.4_preprocessed_sampleMetadata.tsv
inst/extdata/bhklabAnnotationFiles/cell_annotation_all.csv
inst/extdata/bhklabAnnotationFiles/drugs_with_ids.csv
inst/extdata/cellosaurus_fields.tsv
inst/extdata/gCSI/gCSI_GRmetrics_v1.3.tsv
inst/extdata/gCSI/gCSI_sampleMap.txt
inst/extdata/test_cellosaurus_detailed.R
inst/extdata/treatmentMetadata_annotated_pubchem_unichem_chembl.tsv
man/AnnotationGx-package.Rd
man/AttributeInfo.Rd
man/AttributeSet.Rd
man/BioMartClient.Rd
man/CCLE_sampleMetadata.Rd
man/CCLE_treatmentMetadata.Rd
man/CTRP_sampleMetadata.Rd
man/CTRP_treatmentMetadata.Rd
man/DatasetInfo.Rd
man/FilterInfo.Rd
man/GDSC_sampleMetadata.Rd
man/GDSC_treatmentMetadata.Rd
man/MartInfo.Rd
man/annotateCellAccession.Rd
man/annotatePubchemCompound.Rd
man/bm_query_builder.Rd
man/cellosaurusAPIVersion.Rd
man/cellosaurus_fields.Rd
man/cleanCharacterStrings.Rd
man/gCSI_sampleMetadata.Rd
man/gCSI_treatmentMetadata.Rd
man/getChemblFilterTypes.Rd
man/getChemblMechanism.Rd
man/getChemblResourceFields.Rd
man/getChemblResources.Rd
man/getOncotreeMainTypes.Rd
man/getOncotreeTumorTypes.Rd
man/getOncotreeVersions.Rd
man/getPubchemAnnotationHeadings.Rd
man/getPubchemCompound.Rd
man/getPubchemProperties.Rd
man/getPubchemStatus.Rd
man/getUnichemSources.Rd
man/mapCID2Properties.Rd
man/mapCell2Accession.Rd
man/mapCompound2CID.Rd
man/matchNested.Rd
man/queryChemblAPI.Rd
man/queryUnichemCompound.Rd
man/query_hgnc_by_genes.Rd
man/standardize_names.Rd
man/strSplit.Rd
man/unlistNested.Rd
pkgdown/extra.css
tests/testthat.R
tests/testthat/test-utils.R
tests/testthat/test_4_split_utils.R
tests/testthat/test_CancerTargetDiscovery.R
tests/testthat/test_cellosaurus.R
tests/testthat/test_cellosaurus_helpers.R
tests/testthat/test_chembl.R
tests/testthat/test_match-methods.R
tests/testthat/test_oncotree.R
tests/testthat/test_pubchem_bug_fixes.R
tests/testthat/test_pubchem_helpers.R
tests/testthat/test_pubchem_rest_1.R
tests/testthat/test_pubchem_rest_2.R
tests/testthat/test_pubchem_rest_3.R
tests/testthat/test_pubchem_view.R
tests/testthat/test_standardize_names.R
tests/testthat/test_unichem.R
tests/testthat/test_unichem_helpers.R
vignettes/.gitignore
vignettes/Cellosaurus.Rmd
vignettes/ChEMBL.Rmd
vignettes/Introduction.Rmd
vignettes/OncoTree.Rmd
vignettes/PubChemAPI.Rmd
vignettes/Unichem.Rmd
vignettes/articles/AnnotationStandards.Rmd
vignettes/articles/CTRP-Treatment-Annotation.Rmd
