| Type: | Package |
| Version: | 2.0 |
| Date: | 2024-05-24 |
| Title: | Interactive Genome Browser |
| Description: | Creates interactive genome browser. It joins the data analysis power of 'R' and the visualization libraries of 'JavaScript' in one package. Barrios, D. & Prieto, C. (2017) <doi:10.1089/cmb.2016.0213>. |
| URL: | http://d3gb.usal.es |
| License: | GPL-2 | GPL-3 |
| Depends: | R (≥ 3.0.0) |
| Imports: | RSQLite (≥ 1.0.0), DBI (≥ 0.3.1), base64enc |
| NeedsCompilation: | no |
| Maintainer: | Carlos Prieto <cprietos@usal.es> |
| Packaged: | 2024-05-29 10:00:32 UTC; dbarrios |
| Author: | Carlos Prieto 
[aut, cph, cre],
David Barrios
[aut] |
| Repository: | CRAN |
| Date/Publication: | 2024-05-30 08:10:12 UTC |
Interactive genome browsers with R
Description
Create interactive genome browsers with 'R'.
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
Length of human chromosomes based on GRCh37 assembly
Description
Length of human chromosomes based on GRCh37 assembly.
Value
A Data Frame containing length of chromosomes of GRCh37 assembly.
Source
See https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/.
Cytoband information based on GRCh37
Description
A Data Frame containing cytobands of GRCh37 assembly.
Value
A Data Frame containing cytobands of GRCh37 assembly.
Source
See https://grch37.ensembl.org/Homo_sapiens/Location/Genome.
Length of human chromosomes based on GRCh38 assembly
Description
Length of human chromosomes based on GRCh38 assembly.
Value
A Data Frame containing length of chromosomes of GRCh38 assembly.
Source
See https://www.ncbi.nlm.nih.gov/assembly/883148/.
Cytoband information based on GRCh38
Description
A Data Frame containing cytobands of GRCh38 assembly.
Value
A Data Frame containing cytobands of GRCh38 assembly.
Source
See https://www.ensembl.org/Homo_sapiens/Location/Genome.
Length of human chromosomes based on NCBI36 assembly
Description
Length of human chromosomes based on NCBI36 assembly.
Value
A Data Frame containing length of chromosomes of NCBI36 assembly.
Source
See https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.12/.
Creates a genome assembly for genomebrowser or genomemap.
Description
createAssembly create assemblies for their use as parameter of genomebrowser or genomemap.
Usage
createAssembly(name, size)
Arguments
name |
a vector with the chomosome or scaffold names. |
size |
a vector with the chomosome or scaffold sizes. |
Value
a data frame in BED format to be used as an assembly in genomebrowser or genomemap.
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
See Also
The ‘D3GB’ Website: http://d3gb.usal.es
Examples
# A Micromonospora scaffolds' names and sizes
scaffolds <- c("NZ_HF570105.1", "NZ_HF570106.1", "NZ_HF570107.1", "NZ_HF570108.1")
sizes <- c(583, 1327, 241394, 7082520)
# Create an assembly
createAssembly(scaffolds, sizes)
Generates an interactive genome browser.
Description
gbk2genomebrowser creates an interactive genome browser from a GenBank file.
Usage
gbk2genomebrowser(gbkfile)
Arguments
gbkfile |
a "character" string representing the input GenBank file to be represented in the genome browser. |
Value
Object of class genomebrowser.
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
Examples
# Download GenBank file
gbff <- tempfile()
download.file(paste0("https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/297/395/",
"GCF_000297395.2_ASM29739v2/GCF_000297395.2_ASM29739v2_genomic.gbff.gz"),gbff)
# Genome browser generation.
gb <- gbk2genomebrowser(gbff)
plot(gb)
Add track in a gff file to genomebrowser.
Description
genome_addGFF add track in a gff file to genomebrowser.
Usage
genome_addGFF(gb, gfffile)
Arguments
gb |
a genome browser object produced by the function |
gfffile |
a "character" string representing the input gff file to be represented in the genome browser. |
Value
No return value, called for side effects
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
See Also
The ‘D3GB’ Website: http://d3gb.usal.es
genomebrowser, genome_addSequence, genome_addTrack, genome_addVCF.
Examples
# Download fasta file
fasta <- tempfile()
download.file(paste0("https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/297/395/",
"GCF_000297395.2_ASM29739v2/GCF_000297395.2_ASM29739v2_genomic.fna.gz"),fasta)
# Genome browser generation.
gb <- genomebrowser(getAssemblyFromFasta(fasta))
genome_addSequence(gb,fasta)
# Download gff file and add to the genome browser
gff <- tempfile()
download.file(paste0("https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/297/395/",
"GCF_000297395.2_ASM29739v2/GCF_000297395.2_ASM29739v2_genomic.gff.gz"),gff)
genome_addGFF(gb,gff)
plot(gb)
Add genome sequence on Fasta format to genomebrowser.
Description
genome_addSequence add FASTA sequences to genomeviewer.
Usage
genome_addSequence(gb, fastafile)
Arguments
gb |
a genome browser object produced by the function |
fastafile |
a "character" string representing the input Fasta file to be added in the genome browser. |
Value
No return value, called for side effects
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
See Also
The ‘D3GB’ Website: http://d3gb.usal.es
genomebrowser, genome_addGFF, genome_addTrack, genome_addVCF.
Examples
# Download fasta file
fasta <- tempfile()
download.file(paste0("https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/297/395/",
"GCF_000297395.2_ASM29739v2/GCF_000297395.2_ASM29739v2_genomic.fna.gz"),fasta)
# Genome browser generation.
gb <- genomebrowser(getAssemblyFromFasta(fasta))
genome_addSequence(gb,fasta)
plot(gb)
Add tracks to genomebrowser.
Description
genome_addTrack add tracks to genomebrowser.
Usage
genome_addTrack(gb, track, trackname = NULL, type = "gene", color = "#000", scale = NA)
Arguments
gb |
a genome browser object produced by the function |
track |
a "character" string giving the input BED file or a data frame with track information to be represented in the genome browser. |
trackname |
a "character" string giving a name for the track. |
type |
a "character" string with the type of track should be drawn. Possible types are: "gene", "exons", "domain", "value" or "score". |
color |
a "character" string giving the color of the track. |
scale |
a vector with two values which specifies the minimun and maximun limits in the representation of the "score" or "value" tracks. By default maximun and minimun scores are taken as the limits. |
Value
No return value, called for side effects
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
Add VCF tracks to genomebrowser.
Description
genome_addVCF add VCF tracks to genomebrowser.
Usage
genome_addVCF(gb, vcffile, trackname = NULL, show = NULL)
Arguments
gb |
a genome browser object produced by the function |
vcffile |
a "character" string representing the input VCF file to be represented in the genome browser. |
trackname |
a "character" string giving a name for the track. |
show |
a "character" vector giving the info features to display. |
Value
No return value, called for side effects
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
Generates an interactive genome browser.
Description
genome_createLocalMode creates an interactive genome browser to open directly in your browser.
Usage
genome_createLocalMode(gb, dir="GenomeBrowser")
Arguments
gb |
a genome browser object produced by the function |
dir |
a "character" string representing the directory where the graph will be saved. |
Value
The function creates a folder in the working directory of your computer with an HTML document (index.html) which contains the graph. This file can be directly opened with your browser.
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
See Also
The ‘D3GB’ Website: http://d3gb.usal.es
genomebrowser, createAssembly, getAssemblyFromFasta, GRCh37.bands, GRCh38.bands, genome_addGFF, genome_addSequence, genome_addTrack, genome_addVCF.
Examples
# Genome browser generation.
gb <- genomebrowser(GRCh38.bands)
# It creates a genome browser ready to be viewed in your browser.
genome_createLocalMode(gb,dir=tempfile())
Generates an interactive genome browser.
Description
genome_createServerMode creates an interactive genome browser to be shared as a website.
Usage
genome_createServerMode(gb, dir="GenomeBrowser")
Arguments
gb |
a genome browser object produced by the function |
dir |
a "character" string representing the directory where the graph will be saved. |
Value
The function creates a website. Resulting folder should be added to the Apache applications directory. In this way the genome browser will be working as a web site.
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
See Also
The ‘D3GB’ Website: http://d3gb.usal.es
genomebrowser, createAssembly, getAssemblyFromFasta, GRCh37.bands, GRCh38.bands, genome_addGFF, genome_addSequence, genome_addTrack, genome_addVCF.
Examples
# Genome browser generation.
gb <- genomebrowser(GRCh38.bands)
# It creates a website. You can add it to your Apache server.
genome_createServerMode(gb,dir=tempfile())
Generates an interactive genome browser.
Description
genomebrowser creates an interactive genome browser.
Usage
genomebrowser(assembly, tracks = NULL, types = NA, colors = NA, mapTrack = NULL)
Arguments
tracks |
a list of data frames with track information that will be viewed in the genome browser. These data frames should have a BED format with the following columns: chromosome/scaffold, start, end, name, score, strand. |
types |
a "character" vector with type of tracks that will be represented. It should be one of: "gene", "exons", "domain", "value" or "score". |
colors |
a "character" vector with color used for the track representation. |
mapTrack |
a data frame with values to represent on the genome map in BED format: chromosome, start, end, name, value. |
assembly |
a genome assembly data frame. D3GB provides human assemblies (NCBI36, GRCh37, GRCh38), human assemblies with cytobands (GRCh37.bands or GRCh38.bands), or methods for creating your own assembly from a FASTA file |
Value
Object of class genomebrowser.
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
See Also
The ‘D3GB’ Website: http://d3gb.usal.es
createAssembly, getAssemblyFromFasta, GRCh37.bands, GRCh38.bands, genome_addGFF, genome_addSequence, genome_addTrack, genome_addVCF.
Examples
# Genome browser generation.
gb <- genomebrowser(GRCh38.bands)
# Now you can add sequences, tracks, gff or vcf
Create an interative genome map.
Description
genomemap creates an interactive genome map.
Usage
genomemap(assembly, mapTrack = NULL)
Arguments
assembly |
a genome assembly data frame. D3GB provides human assemblies (NCBI36, GRCh37, GRCh38), human assemblies with cytobands (GRCh37.bands or GRCh38.bands), or methods for creating your own assembly from a FASTA file |
mapTrack |
a data frame with values to represent on the genome map in BED format: chromosome, start, end, name, value. |
Value
Object of class genomebrowser.
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
See Also
The ‘D3GB’ Website: http://d3gb.usal.es
createAssembly, getAssemblyFromFasta, GRCh37.bands, GRCh38.bands.
Examples
gm <- genomemap(GRCh38.bands)
Create an assembly from a FASTA file for its use as parameter of genomebrowser or genomemap.
Description
getAssemblyFromFasta create assemblies from a FASTA file for their use as parameter of genomebrowser or genomemap.
Usage
getAssemblyFromFasta(fasta)
Arguments
fasta |
a "character" string representing the input Fasta file to be added in the genome browser. |
Value
a data frame in BED format ready to use as an assembly in genomebrowser or genomemap.
Note
FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes.
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
See Also
The ‘D3GB’ Website: http://d3gb.usal.es
Examples
# Download fasta file
fasta <- tempfile()
download.file(paste0("https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/297/395/",
"GCF_000297395.2_ASM29739v2/GCF_000297395.2_ASM29739v2_genomic.fna.gz"),fasta)
# Assembly generation
getAssemblyFromFasta(fasta)
Function for segmentate tracks in BED format.
Description
segmentation performs a segmentation of track data in bed format in order to enable its effective representation.
Usage
segmentation(track, cell)
Arguments
track |
a Data Frame with genomic features (in BED format). |
cell |
a numeric value with the size of each segment. |
Value
a segmented Data Frame in BED format.
Note
Input file is provided in BED format which is an universal format for genomic features.
Author(s)
David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/
See Also
The ‘D3GB’ Website: http://d3gb.usal.es