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Tag: KaryoploteR
r – HIn karyoploteR, how can I color specific cytobands based on their names?
I would like to ask for some help in using karyoploteR. I am trying to plot some custom genomes with custom cytobands. I want to color each region based on the names. Unfortunately, I was not successful after trying to parse a custom table that would serve as a dictionary….
Bioconductor – rtracklayer
DOI: 10.18129/B9.bioc.rtracklayer R interface to genome annotation files and the UCSC genome browser Bioconductor version: Release (3.6) Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may…
Bioconductor – regioneR (development version)
DOI: 10.18129/B9.bioc.regioneR This is the development version of regioneR; for the stable release version, see regioneR. Association analysis of genomic regions based on permutation tests Bioconductor version: Development (3.19) regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other…
Download stats for experiment package KaryoploteR
Download stats for experiment package KaryoploteR This page was generated on 2023-09-23 22:52:08 -0400 (Sat, 23 Sep 2023). Note that KaryoploteR doesn’t belong to the current release or devel version of Bioconductor anymore. Number of downloads for experiment package KaryoploteR, year by year, from 2023 back to 2009 (years with…
Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation
Abstract Existing monitoring approaches in heart transplantation lack the sensitivity to provide deep molecular assessments to guide management, or require endomyocardial biopsy, an invasive and blind procedure that lacks the precision to reliably obtain biopsy samples from diseased sites. This study examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) as…
Bioconductor – bamsignals
DOI: 10.18129/B9.bioc.bamsignals This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see bamsignals. Extract read count signals from bam files Bioconductor version: 3.16 This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic…
BSgenomeForge with “wrong seq names”
Dear all, I forged a BSgenome with BSgenomeForge for the Indian medaka. This is what the seed file looks like: Package: BSgenome.Omelastigma.NCBI.ASM292280v2 Title: Full genomic sequences for Oryzias melastigma (NCBI assembly ASM292280v2) Description: Full genomic sequences for Oryzias melastigma as provided by NCBI (assembly ASM292280v2, assembly accession GCF_002922805.2). The sequences…
Bioconductor – karyoploteR
DOI: 10.18129/B9.bioc.karyoploteR This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see karyoploteR. Plot customizable linear genomes displaying arbitrary data Bioconductor version: 3.13 karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them….
Two transects reveal remarkable variation in gene flow on opposite ends of a European toad hybrid zone
Abbott R, Albach D, Ansell S, Arntzen JW, Baird SJE, Bierne N, Zinner D (2013) Hybridization and speciation. J Evolut Biol 26:229–246. doi.org/10.1111/j.1420-9101.2012.02599.x Article CAS Google Scholar Arntzen JW (2019) An amphibian species pushed out of Britain by a moving hybrid zone. Mol Ecol 28:5145–5154 Article PubMed PubMed Central Google…
Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics
Yu, Z., Loisel, J., Brosseau, D. P., Beilman, D. W. & Hunt, S. J. Global peatland dynamics since the Last Glacial Maximum. Geophys. Res. Lett. 37, L13402 (2010). van Breemen, N. How Sphagnum bogs down other plants. Trends Ecol. Evol. 10, 270–275 (1995). Article Google Scholar Johnson, M. G. et…
A chromosome-level genome assembly of Plantago ovata
Genome assembly and chromosome identification A Plantago ovata genome reference was generated by utilizing a total of 5.98 M (7 cells, 40.21 Gb, N50 = 10.45 Kb, 50 bp–121.17 Kb) PacBio long reads and 636.5 million (47.74 Gb) Hi-C short-reads. PacBio reads were used to assemble contigs, while Hi-C reads were used to achieve chromosome-level assembly. The final…
karyoploteR: uncircle your genomes
Hi all, I’d like to present karyoploteR, an R/Bioconductor package we have developed to plot any data on any genome in non-circular layouts. The goal of this project was to develop a tool as flexible as Circos, but easier to use and representing genomes as straight lines instead of circles,…
Color label of rainfall plot drawn by KaryoploteR
You can use the standard legend() command as outlined in this issue here: support.bioconductor.org/p/124328/ Minimal example based on bernatgel.github.io/karyoploter_tutorial//Examples/Rainfall/Rainfall.html : library(karyoploteR) somatic.mutations <- read.table(file=”ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl/somatic_mutation_data/Pancreas/Pancreas_raw_mutations_data.txt”, header=FALSE, sep=”t”, stringsAsFactors=FALSE) somatic.mutations <- setNames(somatic.mutations, c(“sample”, “mut.type”, “chr”, “start”, “end”, “ref”, “alt”, “origin”)) somatic.mutations <- split(somatic.mutations, somatic.mutations$sample) sm <- somatic.mutations[[“APGI_1992”]] sm.gr <- toGRanges(sm[,c(“chr”, “start”, “end”,…