DeepBlueR: DeepBlueR

Accessing the DeepBlue Epigenetics Data Server through R.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DeepBlueR")
AuthorFelipe Albrecht, Markus List
Bioconductor views Annotation CpGIsland DNAMethylation DataImport DataRepresentation Epigenetics GeneRegulation GenomeAnnotation Preprocessing ThirdPartyClient
Date of publicationNone
MaintainerFelipe Albrecht <felipe.albrecht@mpi-inf.mpg.de>, Markus List <markus.list@mpi-inf.mpg.de>
LicenseGPL (>=2.0)
Version1.0.11

View on Bioconductor

Man pages

deepblue_aggregate: aggregate

deepblue_batch_export_results: batch_export_results

deepblue_binning: binning

deepblue_cache_status: Report on the cache size and status

deepblue_calculate_enrichment: calculate_enrichment

deepblue_cancel_request: cancel_request

deepblue_chromosomes: chromosomes

deepblue_clear_cache: Clear cache

deepblue_collection_experiments_count: collection_experiments_count

deepblue_column_types: get columns

DeepBlueCommand-class: DeepBlueCommand class

deepblue_commands: commands

deepblue_convert_to_df: convert_to_df

deepblue_convert_to_grange: convert_to_grange

deepblue_count_gene_ontology_terms: count_gene_ontology_terms

deepblue_count_regions: count_regions

deepblue_coverage: coverage

deepblue_delete_request_from_cache: Delete a specific request from the cache

deepblue_diff: diff

deepblue_download_request_data: deepblue_download_request_data

deepblue_download_request_data-DeepBlueCommand-method: deepblue_download_request_data

deepblue_echo: echo

deepblue_export_bed: Export GenomicRanges result as BED file

deepblue_export_meta_data: Export meta data as tab delimited file

deepblue_export_tab: Export a DeepBlue result as ordinary tab delimited file

deepblue_extend: extend

deepblue_extract_ids: extract_ids

deepblue_extract_names: extract_names

deepblue_faceting_experiments: faceting_experiments

deepblue_filter_regions: filter_regions

deepblue_flank: flank

deepblue_format_object_size: Format byte size as human readable units

deepblue_get_biosource_children: get_biosource_children

deepblue_get_biosource_parents: get_biosource_parents

deepblue_get_biosource_related: get_biosource_related

deepblue_get_biosource_synonyms: get_biosource_synonyms

deepblue_get_db: Sets up the DeepBlueR cache and returns a filehash db object

deepblue_get_experiments_by_query: get_experiments_by_query

deepblue_get_regions: get_regions

deepblue_get_request_data: get_request_data

deepblue_info: info

deepblue_input_regions: input_regions

deepblue_intersection: intersection

deepblue_is_biosource: is_biosource

deepblue_liftover: Lift over region results between Genome Assemblies used in...

deepblue_list_annotations: list_annotations

deepblue_list_biosources: list_biosources

deepblue_list_cached_requests: List cached requests

deepblue_list_column_types: list_column_types

deepblue_list_epigenetic_marks: list_epigenetic_marks

deepblue_list_experiments: list_experiments

deepblue_list_expressions: list_expressions

deepblue_list_gene_models: list_gene_models

deepblue_list_genes: list_genes

deepblue_list_genomes: list_genomes

deepblue_list_in_use: list_in_use

deepblue_list_projects: list_projects

deepblue_list_recent_experiments: list_recent_experiments

deepblue_list_requests: list_requests

deepblue_list_samples: list_samples

deepblue_list_similar_biosources: list_similar_biosources

deepblue_list_similar_epigenetic_marks: list_similar_epigenetic_marks

deepblue_list_similar_experiments: list_similar_experiments

deepblue_list_similar_genomes: list_similar_genomes

deepblue_list_similar_projects: list_similar_projects

deepblue_list_similar_techniques: list_similar_techniques

deepblue_list_techniques: list_techniques

deepblue_merge_queries: merge_queries

deepblue_meta_data_to_table: Convert XML structured meta data to table format

deepblue_name_to_id: name_to_id

deepblue_options: options

deepblue_overlap: overlap

deepblue_parse_gtf: deepblue_parse_gtf

deepblue_preview_experiment: preview_experiment

deepblue_query_cache: query_cache

deepblue_query_experiment_type: query_experiment_type

deepblue_reset_options: Reset DeepBlueR options

deepblue_score_matrix: score_matrix

deepblue_search: search

deepblue_select_annotations: select_annotations

deepblue_select_column: select column

deepblue_select_experiments: select_experiments

deepblue_select_expressions: select_expressions

deepblue_select_genes: select_genes

deepblue_select_regions: select_regions

deepblue_switch_get_request_data: switch_get_request_data

deepblue_tiling_regions: tiling_regions

deepblue_wait_request: deepblue_wait_request

show-DeepBlueCommand-method: show DeepBlue command object

xml.rpc: xml.rpc

Functions

deepblue_aggregate Man page
deepblue_batch_export_results Man page
deepblue_binning Man page
deepblue_cache_status Man page
deepblue_calculate_enrichment Man page
deepblue_cancel_request Man page
deepblue_chromosomes Man page
deepblue_clear_cache Man page
deepblue_collection_experiments_count Man page
deepblue_column_types Man page
DeepBlueCommand Man page
DeepBlueCommand-class Man page
deepblue_commands Man page
deepblue_convert_to_df Man page
deepblue_convert_to_grange Man page
deepblue_count_gene_ontology_terms Man page
deepblue_count_regions Man page
deepblue_coverage Man page
deepblue_delete_request_from_cache Man page
deepblue_diff Man page
deepblue_download_request_data Man page
deepblue_download_request_data,DeepBlueCommand-method Man page
deepblue_echo Man page
deepblue_export_bed Man page
deepblue_export_meta_data Man page
deepblue_export_tab Man page
deepblue_extend Man page
deepblue_extract_ids Man page
deepblue_extract_names Man page
deepblue_faceting_experiments Man page
deepblue_filter_regions Man page
deepblue_flank Man page
deepblue_format_object_size Man page
deepblue_get_biosource_children Man page
deepblue_get_biosource_parents Man page
deepblue_get_biosource_related Man page
deepblue_get_biosource_synonyms Man page
deepblue_get_db Man page
deepblue_get_experiments_by_query Man page
deepblue_get_regions Man page
deepblue_get_request_data Man page
deepblue_info Man page
deepblue_input_regions Man page
deepblue_intersection Man page
deepblue_is_biosource Man page
deepblue_liftover Man page
deepblue_list_annotations Man page
deepblue_list_biosources Man page
deepblue_list_cached_requests Man page
deepblue_list_column_types Man page
deepblue_list_epigenetic_marks Man page
deepblue_list_experiments Man page
deepblue_list_expressions Man page
deepblue_list_gene_models Man page
deepblue_list_genes Man page
deepblue_list_genomes Man page
deepblue_list_in_use Man page
deepblue_list_projects Man page
deepblue_list_recent_experiments Man page
deepblue_list_requests Man page
deepblue_list_samples Man page
deepblue_list_similar_biosources Man page
deepblue_list_similar_epigenetic_marks Man page
deepblue_list_similar_experiments Man page
deepblue_list_similar_genomes Man page
deepblue_list_similar_projects Man page
deepblue_list_similar_techniques Man page
deepblue_list_techniques Man page
deepblue_merge_queries Man page
deepblue_meta_data_to_table Man page
deepblue_name_to_id Man page
deepblue_options Man page
deepblue_overlap Man page
deepblue_parse_gtf Man page
deepblue_preview_experiment Man page
deepblue_query_cache Man page
deepblue_query_experiment_type Man page
deepblue_reset_options Man page
deepblue_score_matrix Man page
deepblue_search Man page
deepblue_select_annotations Man page
deepblue_select_column Man page
deepblue_select_experiments Man page
deepblue_select_expressions Man page
deepblue_select_genes Man page
deepblue_select_regions Man page
deepblue_switch_get_request_data Man page
deepblue_tiling_regions Man page
deepblue_wait_request Man page
get_request_data Man page
show,DeepBlueCommand-method Man page
xml.rpc Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/caching.R R/class_DeepBlueCommand.R R/deepblue.R R/export.R R/helperFunctions.R R/internalFunctions.R R/liftover.R R/methods_DeepBlueCommand.R R/options.R R/zzz.R
README.md
build
build/api_auto.template
build/deepblue_r.py
build/examples
build/examples/deepblue.add_annotation.R build/examples/deepblue.add_biosource.R build/examples/deepblue.add_epigenetic_mark.R build/examples/deepblue.add_experiment.R build/examples/deepblue.add_gene_model.R build/examples/deepblue.add_genome.R build/examples/deepblue.add_project.R build/examples/deepblue.add_sample.R build/examples/deepblue.add_sample_from_gsm.R build/examples/deepblue.add_technique.R build/examples/deepblue.add_user_to_project.R build/examples/deepblue.aggregate.R build/examples/deepblue.binning.R build/examples/deepblue.calculate_enrichment.R build/examples/deepblue.cancel_request.R build/examples/deepblue.change_extra_metadata.R build/examples/deepblue.chromosomes.R build/examples/deepblue.clone_dataset.R build/examples/deepblue.collection_experiments_count.R build/examples/deepblue.column_types.R build/examples/deepblue.commands.R build/examples/deepblue.count_gene_ontology_terms.R build/examples/deepblue.count_regions.R build/examples/deepblue.coverage.R build/examples/deepblue.create_column_type_calculated.R build/examples/deepblue.create_column_type_category.R build/examples/deepblue.create_column_type_range.R build/examples/deepblue.create_column_type_simple.R build/examples/deepblue.echo.R build/examples/deepblue.extend.R build/examples/deepblue.extract_ids.R build/examples/deepblue.extract_names.R build/examples/deepblue.faceting_experiments.R build/examples/deepblue.filter_regions.R build/examples/deepblue.find_pattern.R build/examples/deepblue.flank.R build/examples/deepblue.get_biosource_children.R build/examples/deepblue.get_biosource_parents.R build/examples/deepblue.get_biosource_related.R build/examples/deepblue.get_biosource_synonyms.R build/examples/deepblue.get_experiments_by_query.R build/examples/deepblue.get_regions.R build/examples/deepblue.get_request_data.R build/examples/deepblue.get_state.R build/examples/deepblue.info.R build/examples/deepblue.input_regions.R build/examples/deepblue.intersection.R build/examples/deepblue.is_biosource.R build/examples/deepblue.list_annotations.R build/examples/deepblue.list_biosources.R build/examples/deepblue.list_column_types.R build/examples/deepblue.list_epigenetic_marks.R build/examples/deepblue.list_experiments.R build/examples/deepblue.list_expressions.R build/examples/deepblue.list_gene_models.R build/examples/deepblue.list_genes.R build/examples/deepblue.list_genomes.R build/examples/deepblue.list_in_use.R build/examples/deepblue.list_projects.R build/examples/deepblue.list_recent_experiments.R build/examples/deepblue.list_requests.R build/examples/deepblue.list_samples.R build/examples/deepblue.list_similar_biosources.R build/examples/deepblue.list_similar_epigenetic_marks.R build/examples/deepblue.list_similar_experiments.R build/examples/deepblue.list_similar_genomes.R build/examples/deepblue.list_similar_projects.R build/examples/deepblue.list_similar_techniques.R build/examples/deepblue.list_techniques.R build/examples/deepblue.merge_queries.R build/examples/deepblue.name_to_id.R build/examples/deepblue.overlap.R build/examples/deepblue.preview_experiment.R build/examples/deepblue.query_cache.R build/examples/deepblue.query_experiment_type.R build/examples/deepblue.remove.R build/examples/deepblue.score_matrix.R build/examples/deepblue.search.R build/examples/deepblue.select_annotations.R build/examples/deepblue.select_experiments.R build/examples/deepblue.select_expressions.R build/examples/deepblue.select_genes.R build/examples/deepblue.select_regions.R build/examples/deepblue.set_biosource_parent.R build/examples/deepblue.set_biosource_synonym.R build/examples/deepblue.set_project_public.R build/examples/deepblue.tiling_regions.R build/examples/deepblue.upload_chromosome.R build/serialize.R build/update_package.R
build/vignette.rds
demo
demo/00Index
demo/use_case1.R demo/use_case2.R demo/use_case3.R demo/use_case4.R demo/use_case5.R
inst
inst/CITATION
inst/doc
inst/doc/DeepBlueR.R
inst/doc/DeepBlueR.Rmd
inst/doc/DeepBlueR.html
logo.png
man
man/DeepBlueCommand-class.Rd man/deepblue_aggregate.Rd man/deepblue_batch_export_results.Rd man/deepblue_binning.Rd man/deepblue_cache_status.Rd man/deepblue_calculate_enrichment.Rd man/deepblue_cancel_request.Rd man/deepblue_chromosomes.Rd man/deepblue_clear_cache.Rd man/deepblue_collection_experiments_count.Rd man/deepblue_column_types.Rd man/deepblue_commands.Rd man/deepblue_convert_to_df.Rd man/deepblue_convert_to_grange.Rd man/deepblue_count_gene_ontology_terms.Rd man/deepblue_count_regions.Rd man/deepblue_coverage.Rd man/deepblue_delete_request_from_cache.Rd man/deepblue_diff.Rd man/deepblue_download_request_data-DeepBlueCommand-method.Rd man/deepblue_download_request_data.Rd man/deepblue_echo.Rd man/deepblue_export_bed.Rd man/deepblue_export_meta_data.Rd man/deepblue_export_tab.Rd man/deepblue_extend.Rd man/deepblue_extract_ids.Rd man/deepblue_extract_names.Rd man/deepblue_faceting_experiments.Rd man/deepblue_filter_regions.Rd man/deepblue_flank.Rd man/deepblue_format_object_size.Rd man/deepblue_get_biosource_children.Rd man/deepblue_get_biosource_parents.Rd man/deepblue_get_biosource_related.Rd man/deepblue_get_biosource_synonyms.Rd man/deepblue_get_db.Rd man/deepblue_get_experiments_by_query.Rd man/deepblue_get_regions.Rd man/deepblue_get_request_data.Rd man/deepblue_info.Rd man/deepblue_input_regions.Rd man/deepblue_intersection.Rd man/deepblue_is_biosource.Rd man/deepblue_liftover.Rd man/deepblue_list_annotations.Rd man/deepblue_list_biosources.Rd man/deepblue_list_cached_requests.Rd man/deepblue_list_column_types.Rd man/deepblue_list_epigenetic_marks.Rd man/deepblue_list_experiments.Rd man/deepblue_list_expressions.Rd man/deepblue_list_gene_models.Rd man/deepblue_list_genes.Rd man/deepblue_list_genomes.Rd man/deepblue_list_in_use.Rd man/deepblue_list_projects.Rd man/deepblue_list_recent_experiments.Rd man/deepblue_list_requests.Rd man/deepblue_list_samples.Rd man/deepblue_list_similar_biosources.Rd man/deepblue_list_similar_epigenetic_marks.Rd man/deepblue_list_similar_experiments.Rd man/deepblue_list_similar_genomes.Rd man/deepblue_list_similar_projects.Rd man/deepblue_list_similar_techniques.Rd man/deepblue_list_techniques.Rd man/deepblue_merge_queries.Rd man/deepblue_meta_data_to_table.Rd man/deepblue_name_to_id.Rd man/deepblue_options.Rd man/deepblue_overlap.Rd man/deepblue_parse_gtf.Rd man/deepblue_preview_experiment.Rd man/deepblue_query_cache.Rd man/deepblue_query_experiment_type.Rd man/deepblue_reset_options.Rd man/deepblue_score_matrix.Rd man/deepblue_search.Rd man/deepblue_select_annotations.Rd man/deepblue_select_column.Rd man/deepblue_select_experiments.Rd man/deepblue_select_expressions.Rd man/deepblue_select_genes.Rd man/deepblue_select_regions.Rd man/deepblue_switch_get_request_data.Rd man/deepblue_tiling_regions.Rd man/deepblue_wait_request.Rd man/show-DeepBlueCommand-method.Rd man/xml.rpc.Rd
vignettes
vignettes/DeepBlueR.Rmd
vignettes/logo.png

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