Questions tagged [gviz]

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-1 votes
1 answer

Gviz Coverage Plots

This question has also been asked on Biostars I have two bam files from single-cell RNA sequencing mapped to the reference genome using CellRanger, I can view them in IGV and I have a particular ...
1 vote
0 answers

Combining dataTracks in Gviz by averaging or subtraction

I would like to average (and maybe also additional operations such as subtraction) 2 or more DataTracks and plot the result using the Gviz (
0 votes
2 answers

Easy way to create gene plot in gviz?

I would like to create a simple plot of a given human gene containing the main features, e.g. exons, introns, ORFs, transcripts etc. I understand that gviz is a ...
6 votes
1 answer

How to make chromosome color maps for bed ranges

I have genomic .bed file data of 4 different types; type A,B,C,D. These are some examples- Type A: 1 101380000 101710000 A 1 110085000 110320000 A ...
3 votes
1 answer

How to plot genomic.fna fasta file in R using Gviz?

I downloaded the genome of Staph aureus as DNA sequence from NCBI. I would like to visualize it using Gviz. Is Gviz the right tool to visualize genomes? What are the necessary steps from the sequence ...
1 vote
3 answers

How can I install bioconductor-gviz and use it in jupyter notebook?

I tried to install gviz in a conda environment, but that library seems to be incompatible to python and r. I tried to setup a clean environment using ...
2 votes
1 answer

How to plot circular chromosomes with Gviz?

I am using Gviz to plot several tracks. I create a GenomeAxisTrack() and then several AnnotationTrack()s that I feed to ...
7 votes
1 answer

How can I colour boxes in Gviz AnnotationTrack in R?

I'm learning the Gviz bioconductor package, I generate a plot as follows: ...