Showing 10 of total 10 results (show query)
bioc
syntenet:Inference And Analysis Of Synteny Networks
syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.
Maintained by Fabrício Almeida-Silva. Last updated 3 months ago.
softwarenetworkinferencefunctionalgenomicscomparativegenomicsphylogeneticssystemsbiologygraphandnetworkwholegenomenetworkcomparative-genomicsevolutionary-genomicsnetwork-sciencephylogenomicssyntenysynteny-networkcpp
47.0 match 26 stars 6.67 score 12 scripts 1 dependents
tickingclock1992
RIdeogram:Drawing SVG Graphics to Visualize and Map Genome-Wide Data on Idiograms
For whole-genome analysis, idiograms are virtually the most intuitive and effective way to map and visualize the genome-wide information. RIdeogram was developed to visualize and map whole-genome data on idiograms with no restriction of species.
Maintained by Zhaodong Hao. Last updated 4 years ago.
11.0 match 169 stars 7.97 score 62 scriptsbioc
SynExtend:Tools for Working With Synteny Objects
Shared order between genomic sequences provide a great deal of information. Synteny objects produced by the R package DECIPHER provides quantitative information about that shared order. SynExtend provides tools for extracting information from Synteny objects.
Maintained by Nicholas Cooley. Last updated 3 days ago.
geneticsclusteringcomparativegenomicsdataimportfortranopenmp
12.4 match 1 stars 6.42 score 77 scriptsbioc
cogeqc:Systematic quality checks on comparative genomics analyses
cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.
Maintained by Fabrício Almeida-Silva. Last updated 5 months ago.
softwaregenomeassemblycomparativegenomicsfunctionalgenomicsphylogeneticsqualitycontrolnetworkcomparative-genomicsevolutionary-genomics
12.2 match 10 stars 6.08 score 20 scripts
farre-lab
syntenyPlotteR:Genome Synteny Visualization
Draw syntenic relationships between genome assemblies. There are 3 functions which take a tab delimited file containing alignment data for syntenic blocks between genomes to produce either a linear alignment plot, an evolution highway style plot, or a painted ideogram representing syntenic relationships. There is also a function to convert alignment data in the DESCHRAMBLER/inferCAR format to the required data structure.
Maintained by Marta Farre. Last updated 1 years ago.
10.3 match 39 stars 5.57 score 19 scripts
thackl
gggenomes:A Grammar of Graphics for Comparative Genomics
An extension of 'ggplot2' for creating complex genomic maps. It builds on the power of 'ggplot2' and 'tidyverse' adding new 'ggplot2'-style geoms & positions and 'dplyr'-style verbs to manipulate the underlying data. It implements a layout concept inspired by 'ggraph' and introduces tracks to bring tidiness to the mess that is genomics data.
Maintained by Thomas Hackl. Last updated 2 months ago.
biological-datacomparative-genomicsgenomics-visualizationggplot-extensionggplot2
4.4 match 650 stars 9.56 score 123 scriptsbioc
DECIPHER:Tools for curating, analyzing, and manipulating biological sequences
A toolset for deciphering and managing biological sequences.
Maintained by Erik Wright. Last updated 5 days ago.
clusteringgeneticssequencingdataimportvisualizationmicroarrayqualitycontrolqpcralignmentwholegenomemicrobiomeimmunooncologygenepredictionopenmp
3.9 match 8.40 score 1.1k scripts 14 dependents
samilhll
macrosyntR:Draw Ordered Oxford Grids
Use standard genomics file format (BED) and a table of orthologs to illustrate synteny conservation at the genome-wide scale. Significantly conserved linkage groups are identified as described in Simakov et al. (2020) <doi:10.1038/s41559-020-1156-z> and displayed on an Oxford Grid (Edwards (1991) <doi:10.1111/j.1469-1809.1991.tb00394.x>) or a chord diagram as in Simakov et al. (2022) <doi:10.1126/sciadv.abi5884>. The package provides a function that uses a network-based greedy algorithm to find communities (Clauset et al. (2004) <doi:10.1103/PhysRevE.70.066111>) and so automatically order the chromosomes on the plot to improve interpretability.
Maintained by Sami El Hilali. Last updated 9 months ago.
bioinformaticsgenomic-visualizationsgenomics
6.1 match 14 stars 4.85 score 5 scripts
dwinter
pafr:Read, Manipulate and Visualize 'Pairwise mApping Format' Data
Provides functions to read, process and visualize pairwise sequence alignments in the 'PAF' format used by 'minimap2' and other whole-genome aligners. 'minimap2' is described by Li H. (2018) <doi:10.1093/bioinformatics/bty191>.
Maintained by David Winter. Last updated 4 years ago.
3.2 match 71 stars 6.73 score 75 scripts
