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| #' NCBI information for 1000 eukaryotes | ||
| #' | ||
| #' A dataset containing NCBI information of 1000 eukaryotes. The variables are as follows: | ||
| #' | ||
| #' @format A data frame with 1000 rows and 19 variables: | ||
| #' \describe{ | ||
| #' \item{X.Organism.Name}{Organism name at the species level} | ||
| #' \item{taxid}{NCBI taxid} | ||
| #' \item{BioProject.Accession}{BioProject Accession number (from BioProject database)} | ||
| #' \item{BioProject.ID}{BioProject ID} | ||
| #' \item{Group}{Commonly used organism groups: Animals, Fungi, Plants, Protists} | ||
| #' \item{SubGroup}{NCBI Taxonomy level below group: Mammals, Birds, Fishes, Flatworms, Insects, Amphibians, Reptiles, Roundworms, Ascomycetes, Basidiomycetes, Land Plants, Green Algae, Apicomplexans, Kinetoplasts} | ||
| #' \item{Size..Mb.}{Total length of DNA submitted for the project} | ||
| #' \item{GC.}{Percent of nitrogenous bases (guanine or cytosine) in DNA submitted for the project} | ||
| #' \item{Assembly.Accession}{Name of the genome assembly (from NCBI Assembly database)} | ||
| #' \item{Replicons}{Number of replicons in the assembly} | ||
| #' \item{WGS}{Four-letter Accession prefix followed by version as defined in WGS division of GenBank/INSDC} | ||
| #' \item{Scaffolds}{Number of scaffolds in the assembly} | ||
| #' \item{Genes}{Number of Genes annotated in the assembly} | ||
| #' \item{Proteins}{Number of Proteins annotated in the assembly} | ||
| #' \item{Release.Date}{First public sequence release for the project} | ||
| #' \item{Modify.Date}{Sequence modification date for the project} | ||
| #' \item{Status}{Highest level of assembly: <br> Chromosomes: one or more chromosomes are assembled<br> Scaffolds or contigs: sequence assembled but no chromosomes} | ||
| #' \item{Center}{Origin of the sample} | ||
| #' \item{BioSample.Accession}{BioSample Accession number} | ||
| #' } | ||
| #' @usage data(eukaryotes_1000) | ||
| "eukaryotes_1000" | ||
|
|
||
| #' NCBI information for 80 eukaryotes | ||
| #' | ||
| #' A dataset containing NCBI information of 80 eukaryotes. The variables are as follows: | ||
| #' | ||
| #' @format A data frame with 80 rows and 19 variables: | ||
| #' \describe{ | ||
| #' \item{X.Organism.Name}{Organism name at the species level} | ||
| #' \item{taxid}{NCBI taxid} | ||
| #' \item{BioProject.Accession}{BioProject Accession number (from BioProject database)} | ||
| #' \item{BioProject.ID}{BioProject ID} | ||
| #' \item{Group}{Commonly used organism groups: Animals, Fungi, Plants, Protists} | ||
| #' \item{SubGroup}{NCBI Taxonomy level below group: Mammals, Birds, Fishes, Flatworms, Insects, Amphibians, Reptiles, Roundworms, Ascomycetes, Basidiomycetes, Land Plants, Green Algae, Apicomplexans, Kinetoplasts} | ||
| #' \item{Size..Mb.}{Total length of DNA submitted for the project} | ||
| #' \item{GC.}{Percent of nitrogenous bases (guanine or cytosine) in DNA submitted for the project} | ||
| #' \item{Assembly.Accession}{Name of the genome assembly (from NCBI Assembly database)} | ||
| #' \item{Replicons}{Number of replicons in the assembly} | ||
| #' \item{WGS}{Four-letter Accession prefix followed by version as defined in WGS division of GenBank/INSDC} | ||
| #' \item{Scaffolds}{Number of scaffolds in the assembly} | ||
| #' \item{Genes}{Number of Genes annotated in the assembly} | ||
| #' \item{Proteins}{Number of Proteins annotated in the assembly} | ||
| #' \item{Release.Date}{First public sequence release for the project} | ||
| #' \item{Modify.Date}{Sequence modification date for the project} | ||
| #' \item{Status}{Highest level of assembly: <br> Chromosomes: one or more chromosomes are assembled<br> Scaffolds or contigs: sequence assembled but no chromosomes} | ||
| #' \item{Center}{Origin of the sample} | ||
| #' \item{BioSample.Accession}{BioSample Accession number} | ||
| #' } | ||
| #' @usage data(eukaryotes_80) | ||
| "eukaryotes_80" | ||
|
|
||
| #' Transformation in a LifemapR format of NCBI information for 1000 eukaryotes | ||
| #' | ||
| #' A dataset containing NCBI information of 1000 eukaryotes. The variables are as follows: | ||
| #' | ||
| #' @format A lifemap object - a list containing the basemap used to fetch data and df, a data frame with 2760 rows and 26 variables: | ||
| #' \describe{ | ||
| #' \item{X.Organism.Name}{Organism name at the species level} | ||
| #' \item{taxid}{NCBI taxid} | ||
| #' \item{BioProject.Accession}{BioProject Accession number (from BioProject database)} | ||
| #' \item{BioProject.ID}{BioProject ID} | ||
| #' \item{Group}{Commonly used organism groups: Animals, Fungi, Plants, Protists} | ||
| #' \item{SubGroup}{NCBI Taxonomy level below group: Mammals, Birds, Fishes, Flatworms, Insects, Amphibians, Reptiles, Roundworms, Ascomycetes, Basidiomycetes, Land Plants, Green Algae, Apicomplexans, Kinetoplasts} | ||
| #' \item{Size..Mb.}{Total length of DNA submitted for the project} | ||
| #' \item{GC.}{Percent of nitrogenous bases (guanine or cytosine) in DNA submitted for the project} | ||
| #' \item{Assembly.Accession}{Name of the genome assembly (from NCBI Assembly database)} | ||
| #' \item{Replicons}{Number of replicons in the assembly} | ||
| #' \item{WGS}{Four-letter Accession prefix followed by version as defined in WGS division of GenBank/INSDC} | ||
| #' \item{Scaffolds}{Number of scaffolds in the assembly} | ||
| #' \item{Genes}{Number of Genes annotated in the assembly} | ||
| #' \item{Proteins}{Number of Proteins annotated in the assembly} | ||
| #' \item{Release.Date}{First public sequence release for the project} | ||
| #' \item{Modify.Date}{Sequence modification date for the project} | ||
| #' \item{Status}{Highest level of assembly: <br> Chromosomes: one or more chromosomes are assembled<br> Scaffolds or contigs: sequence assembled but no chromosomes} | ||
| #' \item{Center}{Origin of the sample} | ||
| #' \item{BioSample.Accession}{BioSample Accession number} | ||
| #' \item{lon}{longitude of taxids on a specific basemap} | ||
| #' \item{lat}{latitude of taxids on a specific basemap} | ||
| #' \item{sci_name}{scientific name of taxids} | ||
| #' \item{zoom}{zoom of taxids on a specific basemap} | ||
| #' \item{ascend}{the list of all ancestors of taxids on a specific basemap} | ||
| #' \item{type}{either "requested" if the taxid was given, "ancestor" if gotten from the database} | ||
| #' \item{ancestor}{the direct ancestor oftaxids on a specific basemap} | ||
| #' } | ||
| #' @usage data(LM_eukaryotes) | ||
| "LM_eukaryotes" | ||
|
|
||
| #' Kraken results | ||
| #' | ||
| #' A dataset containing NCBI information of 1000 eukaryotes. The variables are as follows: | ||
| #' | ||
| #' @format A data frame with 4427 rows and 6 variables: | ||
| #' \describe{ | ||
| #' \item{coverage_percent}{Percentage of fragments covered by the clade rooted at this taxon} | ||
| #' \item{coverage_number}{Number of fragments covered by the clade rooted at this taxon} | ||
| #' \item{fragment_number}{Number of fragments assigned directly to this taxon} | ||
| #' \item{rank}{A rank code, indicating (U)nclassified, (R)oot, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. Taxa that are not at any of these 10 ranks have a rank code that is formed by using the rank code of the closest ancestor rank with a number indicating the distance from that rank. E.g., "G2" is a rank code indicating a taxon is between genus and species and the grandparent taxon is at the genus rank.} | ||
| #' \item{taxid}{NCBI taxonomic ID number} | ||
| #' \item{name}{Indented scientific name} | ||
| #' } | ||
| #' @usage data(kraken_res) | ||
| "kraken_res" | ||
|
|
||
|
|
||
| #' Genomic results | ||
| #' | ||
| #' A dataset containing information on Genome size and TE content for 808 taxids | ||
| #' | ||
| #' @format A data frame with 808 rows and 3 variables: | ||
| #' \describe{ | ||
| #' \item{taxid}{NCBI taxid} | ||
| #' \item{Genome_size}{the Genome size in pb} | ||
| #' \item{TEcontent_bp}{the transposable element content in pb} | ||
| #' } | ||
| #' @usage data(gen_res) | ||
| "gen_res" | ||
| #' NCBI information for 1000 eukaryotes | ||
| #' | ||
| #' A dataset containing NCBI information of 1000 eukaryotes. The variables are as follows: | ||
| #' | ||
| #' @format A data frame with 1000 rows and 19 variables: | ||
| #' \describe{ | ||
| #' \item{X.Organism.Name}{Organism name at the species level} | ||
| #' \item{taxid}{NCBI taxid} | ||
| #' \item{BioProject.Accession}{BioProject Accession number (from BioProject database)} | ||
| #' \item{BioProject.ID}{BioProject ID} | ||
| #' \item{Group}{Commonly used organism groups: Animals, Fungi, Plants, Protists} | ||
| #' \item{SubGroup}{NCBI Taxonomy level below group: Mammals, Birds, Fishes, Flatworms, Insects, Amphibians, Reptiles, Roundworms, Ascomycetes, Basidiomycetes, Land Plants, Green Algae, Apicomplexans, Kinetoplasts} | ||
| #' \item{Size..Mb.}{Total length of DNA submitted for the project} | ||
| #' \item{GC.}{Percent of nitrogenous bases (guanine or cytosine) in DNA submitted for the project} | ||
| #' \item{Assembly.Accession}{Name of the genome assembly (from NCBI Assembly database)} | ||
| #' \item{Replicons}{Number of replicons in the assembly} | ||
| #' \item{WGS}{Four-letter Accession prefix followed by version as defined in WGS division of GenBank/INSDC} | ||
| #' \item{Scaffolds}{Number of scaffolds in the assembly} | ||
| #' \item{Genes}{Number of Genes annotated in the assembly} | ||
| #' \item{Proteins}{Number of Proteins annotated in the assembly} | ||
| #' \item{Release.Date}{First public sequence release for the project} | ||
| #' \item{Modify.Date}{Sequence modification date for the project} | ||
| #' \item{Status}{Highest level of assembly: <br> Chromosomes: one or more chromosomes are assembled<br> Scaffolds or contigs: sequence assembled but no chromosomes} | ||
| #' \item{Center}{Origin of the sample} | ||
| #' \item{BioSample.Accession}{BioSample Accession number} | ||
| #' } | ||
| #' @usage data(eukaryotes_1000) | ||
| "eukaryotes_1000" | ||
|
|
||
| #' NCBI information for 80 eukaryotes | ||
| #' | ||
| #' A dataset containing NCBI information of 80 eukaryotes. The variables are as follows: | ||
| #' | ||
| #' @format A data frame with 80 rows and 19 variables: | ||
| #' \describe{ | ||
| #' \item{X.Organism.Name}{Organism name at the species level} | ||
| #' \item{taxid}{NCBI taxid} | ||
| #' \item{BioProject.Accession}{BioProject Accession number (from BioProject database)} | ||
| #' \item{BioProject.ID}{BioProject ID} | ||
| #' \item{Group}{Commonly used organism groups: Animals, Fungi, Plants, Protists} | ||
| #' \item{SubGroup}{NCBI Taxonomy level below group: Mammals, Birds, Fishes, Flatworms, Insects, Amphibians, Reptiles, Roundworms, Ascomycetes, Basidiomycetes, Land Plants, Green Algae, Apicomplexans, Kinetoplasts} | ||
| #' \item{Size..Mb.}{Total length of DNA submitted for the project} | ||
| #' \item{GC.}{Percent of nitrogenous bases (guanine or cytosine) in DNA submitted for the project} | ||
| #' \item{Assembly.Accession}{Name of the genome assembly (from NCBI Assembly database)} | ||
| #' \item{Replicons}{Number of replicons in the assembly} | ||
| #' \item{WGS}{Four-letter Accession prefix followed by version as defined in WGS division of GenBank/INSDC} | ||
| #' \item{Scaffolds}{Number of scaffolds in the assembly} | ||
| #' \item{Genes}{Number of Genes annotated in the assembly} | ||
| #' \item{Proteins}{Number of Proteins annotated in the assembly} | ||
| #' \item{Release.Date}{First public sequence release for the project} | ||
| #' \item{Modify.Date}{Sequence modification date for the project} | ||
| #' \item{Status}{Highest level of assembly: <br> Chromosomes: one or more chromosomes are assembled<br> Scaffolds or contigs: sequence assembled but no chromosomes} | ||
| #' \item{Center}{Origin of the sample} | ||
| #' \item{BioSample.Accession}{BioSample Accession number} | ||
| #' } | ||
| #' @usage data(eukaryotes_80) | ||
| "eukaryotes_80" | ||
|
|
||
| #' Transformation in a LifemapR format of NCBI information for 1000 eukaryotes | ||
| #' | ||
| #' A dataset containing NCBI information of 1000 eukaryotes. The variables are as follows: | ||
| #' | ||
| #' @format A lifemap object - a list containing the basemap used to fetch data and df, a data frame with 2760 rows and 26 variables: | ||
| #' \describe{ | ||
| #' \item{X.Organism.Name}{Organism name at the species level} | ||
| #' \item{taxid}{NCBI taxid} | ||
| #' \item{BioProject.Accession}{BioProject Accession number (from BioProject database)} | ||
| #' \item{BioProject.ID}{BioProject ID} | ||
| #' \item{Group}{Commonly used organism groups: Animals, Fungi, Plants, Protists} | ||
| #' \item{SubGroup}{NCBI Taxonomy level below group: Mammals, Birds, Fishes, Flatworms, Insects, Amphibians, Reptiles, Roundworms, Ascomycetes, Basidiomycetes, Land Plants, Green Algae, Apicomplexans, Kinetoplasts} | ||
| #' \item{Size..Mb.}{Total length of DNA submitted for the project} | ||
| #' \item{GC.}{Percent of nitrogenous bases (guanine or cytosine) in DNA submitted for the project} | ||
| #' \item{Assembly.Accession}{Name of the genome assembly (from NCBI Assembly database)} | ||
| #' \item{Replicons}{Number of replicons in the assembly} | ||
| #' \item{WGS}{Four-letter Accession prefix followed by version as defined in WGS division of GenBank/INSDC} | ||
| #' \item{Scaffolds}{Number of scaffolds in the assembly} | ||
| #' \item{Genes}{Number of Genes annotated in the assembly} | ||
| #' \item{Proteins}{Number of Proteins annotated in the assembly} | ||
| #' \item{Release.Date}{First public sequence release for the project} | ||
| #' \item{Modify.Date}{Sequence modification date for the project} | ||
| #' \item{Status}{Highest level of assembly: <br> Chromosomes: one or more chromosomes are assembled<br> Scaffolds or contigs: sequence assembled but no chromosomes} | ||
| #' \item{Center}{Origin of the sample} | ||
| #' \item{BioSample.Accession}{BioSample Accession number} | ||
| #' \item{lon}{longitude of taxids on a specific basemap} | ||
| #' \item{lat}{latitude of taxids on a specific basemap} | ||
| #' \item{sci_name}{scientific name of taxids} | ||
| #' \item{zoom}{zoom of taxids on a specific basemap} | ||
| #' \item{ascend}{the list of all ancestors of taxids on a specific basemap} | ||
| #' \item{type}{either "requested" if the taxid was given, "ancestor" if gotten from the database} | ||
| #' \item{ancestor}{the direct ancestor oftaxids on a specific basemap} | ||
| #' } | ||
| #' @usage data(LM_eukaryotes) | ||
| "LM_eukaryotes" | ||
|
|
||
| #' Kraken results | ||
| #' | ||
| #' A dataset containing NCBI information of 1000 eukaryotes. The variables are as follows: | ||
| #' | ||
| #' @format A data frame with 4427 rows and 6 variables: | ||
| #' \describe{ | ||
| #' \item{coverage_percent}{Percentage of fragments covered by the clade rooted at this taxon} | ||
| #' \item{coverage_number}{Number of fragments covered by the clade rooted at this taxon} | ||
| #' \item{fragment_number}{Number of fragments assigned directly to this taxon} | ||
| #' \item{rank}{A rank code, indicating (U)nclassified, (R)oot, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. Taxa that are not at any of these 10 ranks have a rank code that is formed by using the rank code of the closest ancestor rank with a number indicating the distance from that rank. E.g., "G2" is a rank code indicating a taxon is between genus and species and the grandparent taxon is at the genus rank.} | ||
| #' \item{taxid}{NCBI taxonomic ID number} | ||
| #' \item{name}{Indented scientific name} | ||
| #' } | ||
| #' @usage data(kraken_res) | ||
| "kraken_res" | ||
|
|
||
|
|
||
| #' Genomic results | ||
| #' | ||
| #' A dataset containing information on Genome size and TE content for 808 taxids | ||
| #' | ||
| #' @format A data frame with 808 rows and 3 variables: | ||
| #' \describe{ | ||
| #' \item{taxid}{NCBI taxid} | ||
| #' \item{Genome_size}{the Genome size in pb} | ||
| #' \item{TEcontent_bp}{the transposable element content in pb} | ||
| #' } | ||
| #' @usage data(gen_res) | ||
| "gen_res" |