Package: LDWeaver 1.5.2

LDWeaver: Genomewide Epistasis Analysis on Bacteria

Perform genomewide epistasis analysis by evaluating the LD structure in bacteria.

Authors:Sudaraka Mallawaarachchi [aut, cre]

LDWeaver_1.5.2.tar.gz
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LDWeaver_1.5.2.tgz(r-4.6-x86_64)LDWeaver_1.5.2.tgz(r-4.6-arm64)
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LDWeaver_1.5.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
LDWeaver/json (API)

# Install 'LDWeaver' in R:
install.packages('LDWeaver', repos = c('https://sudaraka88.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sudaraka88/ldweaver/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

softwarebacterial-genome-analysisbioinformaticsepistasis-analysislinkage-disequilibriummicrobial-genomicscpp

3.18 score 15 stars 4 scripts 24 exports 133 dependencies

Last updated from:05b77d6221. Checks:11 WARNING, 2 OK, 2 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING532
linux-devel-x86_64WARNING692
source / vignettesOK292
linux-release-arm64WARNING568
linux-release-x86_64WARNING516
macos-release-arm64WARNING427
macos-release-x86_64WARNING784
macos-oldrel-arm64FAIL93
macos-oldrel-x86_64FAIL223
windows-devel-arm64WARNING829
windows-devel-x86_64WARNING764
windows-release-arm64WARNING822
windows-release-x86_64WARNING577
windows-oldrel-x86_64WARNING681
wasm-releaseOK216

Exports:analyse_long_range_linkscleanupcreate_networkcreate_network_for_genecreate_tanglegramestimate_Hamming_distance_weightsestimate_variation_in_CDSgenerate_Links_SNPS_fastagenomewide_LDMapLDWeavermake_gwes_plotsparse_fasta_alignmentparse_fasta_SNP_alignmentparse_genbank_fileparse_gff_fileperform_MI_computationperform_snpEff_annotationsread_AnnotatedLinksread_LongRangeLinksread_ShortRangeLinksread_TopHitssnpdat_to_faview_treewrite_output_for_gwes_explorer

Dependencies:abindAnnotationDbiapeaskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemchromoMapcigarilloclicodetoolscpp11crayoncurldata.tableDBIDelayedArraydigestdplyrevaluatefarverfastclusterfastmapfitdistrplusfloatfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtableheatmap3highrhtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixExtraMatrixGenericsmatrixStatsmemoisemimenlmeopensslpillarpkgconfigplyrpngpolyclippurrrR6rappdirsRColorBrewerRcppRcppArmadilloRCurlrestfulrRhpcBLASctlRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidygraphtidyrtidyselecttinytextweenrUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
._legendfun2._legendfun2
.mat.mat
.rescale01.rescale01
analyse_long_range_linksanalyse_long_range_links
cleanupcleanup
cleanup_supportcleanup_support
create_networkcreate_network
create_network_for_genecreate_network_for_gene
create_tanglegramcreate_tanglegram
estimate_Hamming_distance_weightsestimate_Hamming_distance_weights
estimate_variation_in_CDSestimate_variation_in_CDS
GBAccession ID classGBAccession GBAccession-class
GenBank FileGBFile-class GBKFile-class GenBankFile-class
GenBank data objects.GenBankRecord-class
generate_Links_SNPS_fastagenerate_Links_SNPS_fasta
genomewide_LDMapgenomewide_LDMap
LDWeaverLDWeaver
make_gwes_plotsmake_gwes_plots
extractSNP_from_MSAparse_fasta_alignment
extractSNPs_from_SNP_MSAparse_fasta_SNP_alignment
parse_genbank_fileparse_genbank_file
parse_gff_fileparse_gff_file
perform_MI_computationperform_MI_computation
perform_snpEff_annotationsperform_snpEff_annotations
read_AnnotatedLinksread_AnnotatedLinks
read_GFF3_Annotationread_GFF3_Annotation
read_LongRangeLinksread_LongRangeLinks
read_ReferenceFastaread_ReferenceFasta
read_ShortRangeLinksread_ShortRangeLinks
read_TopHitsread_TopHits
runARACNErunARACNE
snpdat_to_fasnpdat_to_fa
view_treeview_tree
write_output_for_gwes_explorerwrite_output_for_gwes_explorer