Package: syntenet 1.7.0

Fabrício Almeida-Silva

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.

Authors:Fabrício Almeida-Silva [aut, cre], Tao Zhao [aut], Kristian K Ullrich [aut], Yves Van de Peer [aut]

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syntenet.pdf |syntenet.html✨
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NEWS

# Install 'syntenet' in R:
install.packages('syntenet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/almeidasilvaf/syntenet/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • angiosperm_phylogeny - Microsynteny-based angiosperm phylogeny.
  • annotation - Filtered genome annotation for Ostreococcus sp. species
  • blast_list - List of data frames containing BLAST-like tabular output
  • clusters - Synteny network clusters of BUSCO genes for 25 eudicot species
  • edges - Synteny network of Ostreococcus genomes represented as an edge list
  • network - Synteny network of BUSCO genes for 25 eudicot species
  • proteomes - Filtered proteomes of Ostreococcus sp. species
  • scerevisiae_annot - Genome annotation of the yeast species S. cerevisiae
  • scerevisiae_diamond - Intraspecies DIAMOND output for S. cerevisiae

On BioConductor:syntenet-1.7.0(bioc 3.20)syntenet-1.6.0(bioc 3.19)

bioconductor-package

27 exports 0.91 score 117 dependencies 1 dependents

Last updated 2 months agofrom:2b17e15a74

Exports:binarize_and_transposecheck_inputcluster_networkcollapse_protein_idscreate_species_id_tablediamond_is_installedexport_sequencesfasta2AAStringSetlistfind_GS_clustersgff2GRangesListinfer_microsynteny_phylogenyinfer_syntenetinterspecies_syntenyintraspecies_syntenyiqtree_is_installediqtree_versionlast_is_installedparse_collinearityphylogenomic_profileplot_networkplot_profilesprocess_inputprofiles2phyliprcpp_mcscanx_fileread_diamondrun_diamondrun_last

Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsbriobslibcachemcallrclicodacodetoolscolorspacecpp11crayoncurlDelayedArraydescdiffobjdigestevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggnetworkggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttrigraphintergraphIRangesisobandjquerylibjsonliteknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnetworknetworkD3nlmeopensslpheatmappillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR6rappdirsRColorBrewerRcppRCurlrematch2restfulrRhtslibrjsonrlangrmarkdownrprojrootRsamtoolsrtracklayerS4ArraysS4VectorssassscalessnasnowSparseArraystatnet.commonSummarizedExperimentsystestthattibbletinytexUCSC.utilsutf8vctrsviridisLitewaldowithrxfunXMLXVectoryamlzlibbioc

Inference and Analysis of Synteny Networks

Fabricio Almeida-Silva, Tao Zhao, Kristian K Ullrich, Yves Van de Peer

Rendered fromsyntenet.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2024-03-20
Started: 2022-03-31

Readme and manuals

Help Manual

Help pageTopics
Microsynteny-based angiosperm phylogeny.angiosperm_phylogeny
Filtered genome annotation for Ostreococcus sp. speciesannotation
Binarize and transpose the phylogenomic profile matrixbinarize_and_transpose
List of data frames containing BLAST-like tabular outputblast_list
Check if input objects are ready for further analysescheck_input
Cluster the synteny network using the Infomap algorithmcluster_network
Synteny network clusters of BUSCO genes for 25 eudicot speciesclusters
Collapse protein IDs into gene IDs in sequence names of AAStringSet objectscollapse_protein_ids
Create a data frame of species IDs (3-5-character abbreviations)create_species_id_table
Check if DIAMOND is installeddiamond_is_installed
Synteny network of Ostreococcus genomes represented as an edge listedges
Export processed sequences as FASTA filesexport_sequences
Read FASTA files in a directory as a list of AAStringSet objectsfasta2AAStringSetlist
Find group-specific clusters based on user-defined species classificationfind_GS_clusters
Read GFF/GTF files in a directory as a GRangesList objectgff2GRangesList
Infer microsynteny-based phylogeny with IQTREEinfer_microsynteny_phylogeny
Infer synteny networkinfer_syntenet
Detect interspecies syntenyinterspecies_synteny
Detect intraspecies syntenyintraspecies_synteny
Check if IQTREE is installediqtree_is_installed
Get IQ-TREE versioniqtree_version
Check if last is installedlast_is_installed
Synteny network of BUSCO genes for 25 eudicot speciesnetwork
Parse .collinearity files obtained with MCScanparse_collinearity
Perform phylogenomic profiling for synteny network clustersphylogenomic_profile
Plot networkplot_network
Plot a heatmap of phylogenomic profilesplot_profiles
Process sequence dataprocess_input
Save the transposed binary profiles matrix to a file in PHYLIP formatprofiles2phylip
Filtered proteomes of Ostreococcus sp. speciesproteomes
rcpp_mcscanx_filercpp_mcscanx_file
Read DIAMOND/BLAST tables as a list of data framesread_diamond
Wrapper to run DIAMOND from an R sessionrun_diamond
Wrapper to run last from an R sessionrun_last
Genome annotation of the yeast species S. cerevisiaescerevisiae_annot
Intraspecies DIAMOND output for S. cerevisiaescerevisiae_diamond