Gviz

[…] fdr < 0.05., ggplot2 (wickham, 2012) and ggrepel (https://cran.r-project.org/web/packages/ggrepel/index.html) r libraries were used for scatterplots. gene model diagrams were generated using the gviz package []. density plots were generated with the lsd package (https://cran.r-project.org/web/packages/lsd/index.html)., linear rna-seq reads were mapped to the c. elegans ce11 annotation using […]

[…] 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 (). 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, for more details see […]

[…] generated using seqminer () and ngsplot (), using default settings, respectively. all other plots were generated using r (http://www.r-project.org) (). genome browsers snapshots were generated using gviz biocondutor package ()., wildtype s2 cells (120 × 106 cells) were harvested. nuclei were isolated and the immunoprecipitation was carried out as previously described (). the immunoprecipitated […]

[…] were compared to the aforementioned comparison snp set using a 2-sided fisher’s exact test. visualizations highlighting functional annotations of selected 3-snp haplotypes were created with the “gviz” r/bioconductor package., the genetic data analyzed in this study are available in the european genome-phenome archive under study accession number egas00001002915 […]

[…] a value of 0.9. peaks were annotated based on nearest transcription start site (tss) using the bioconductor package chippeakanno (zhu et al., ) and chipseeker (yu et al., ) and visualized using the gviz package (hahne and ivanek, )., the sp8 chipseq data presented in the “results” section were obtained using the goat polyclonal anti-sp8 antibody. these results were confirmed with a sp8 chipseq […]

[…] # uncomment the following line to install packages #bioclite(c("clusterprofiler", "deseq2", "genomicfeatures", "genomicinteractions", "genomicranges", "ggplot2", "gviz", "gwascat", "interactionset", "recount", "pheatmap", "rcolorbrewer", "rtracklayer", "r.utils", "splitstackshape", "variantannotation")) , we start with a common scenario: we ran a rna-seq […]

[…] coverage tracks of atac signals we created normalized bigwig files using the homer v4.9.1 command makeucscfile with a specified fragment length of the exact read length and used the bioconductor gviz v1.20.0 package for visualization (). chromatin accessibility of degs was inferred by comparing log-transformed mean counts (cpm) of the accessible regions annotated to the respective genes […]

[…] (logfc) determined the differences between libraries (control, red and maternal nano-tio2 exposed, blue) within the mds plots (fig. ). to visualize read coverage, the r packages chippeakanno and gviz were installed []. complex, differential binding was assessed for both the h3k4me3 (fig. ) and h3k27me3 (fig. ) binding loci. together, these results suggest that the immunoprecipitation […]