Gviz

[…] obtained for contigs of interest using rast (36). regions of similarity between host and clone dna were identified using mauve (37). data analyses were performed in r, including packages rsamtools, gviz, ape, and genoplotr., raw sequence data have been deposited at the ncbi sequence read archive under accession numbers srx3141910 (clgm3 clone 2) and srx3141914 (clgm3 clone 5). sequence data […]

[…] using fastq-multx (https://github.com/brwnj/fastq-multx), and aligned using bwa as described above. we then inspected read alignments from selected, error-prone markers using the r package gviz (hahne and ivanek 2016). when we analyzed the 10 f2 individuals that showed the highest number of single heterozygous genotypes flanked on both sides by nipponbare alleles (aha-type error, […]

[…] in order to generate cumulative average binding profiles. for representation in genome browsers, profiles were additionally smoothed using kernel regression estimates. data were visualized using the gviz bioconductor package., for comparison with other transcription factor binding data we downloaded processed binding data from chip-experiments for dsumo, pita, zipic, polycomb, ibf1, cp190 und […]

[…] sweep region. we used annovar52, again with the ensembl genes database, to annotate variants with respect to their location and potential effects on protein-coding genes. figure 2 was made with the gviz package., kauaian chickens' sequences were phased jointly using shapeit53 and incorporating the sex-averaged recombination map for all chicken populations combined published in elferink et […]

[…] ucsc browser at the url http://genome.ucsc.edu/cgi-bin/hgtracks?db=saccer3&huburl=https://labs.genetics.ucla.edu/kruglyak/trackhub/hub.txt. the track plots in figure 7 were generated using the gviz r package [62]., we are grateful to hunter fraser, carlo artieri, joel mcmanus, joshua bloom, sebastian treusch, j.j. emerson, casey brown, three anonymous reviewers, and members of the kruglyak […]