Package: atSNP 1.23.0

Sunyoung Shin

atSNP: Affinity test for identifying regulatory SNPs

atSNP performs affinity tests of motif matches with the SNP or the reference genomes and SNP-led changes in motif matches.

Authors:Chandler Zuo [aut], Sunyoung Shin [aut, cre], Sunduz Keles [aut]

atSNP_1.23.0.tar.gz
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atSNP_1.23.0.tar.gz(r-4.5-noble)atSNP_1.23.0.tar.gz(r-4.4-noble)
atSNP_1.23.0.tgz(r-4.4-emscripten)
atSNP.pdf |atSNP.html✨
atSNP/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/sunyoungshin/atsnp/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • encode_motif - A motif library containing 2065 motifs downloaded from http://compbio.mit.edu/encode-motifs/motifs.txt.
  • encode_motifinfo - The information for the motif library downloaded from http://compbio.mit.edu/encode-motifs/motifs.txt.
  • jaspar_motif - A motif library containing 593 motifs downloaded from http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_all .txt.
  • jaspar_motifinfo - The information for the motif library downloaded from http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_all .txt.
  • motif_library - A sample motif library.
  • motif_match - Composit logo plotting input containing motif scores, the matching subsequences and the augmented matching subsequences on SNP and reference allele
  • motif_scores - Scores for the sample snp data computed based on the motif data.
  • prior - Default stationary distribution for nucleotide sequences in the reference genome.
  • snpInfo - A data set for SNP information.
  • snp_tbl - A data frame for SNP information.
  • transition - Default transition probability matrix for nucleotide sequences in the reference genome.

On BioConductor:atSNP-1.23.0(bioc 3.21)atSNP-1.22.0(bioc 3.20)

softwarechipseqgenomeannotationmotifannotationvisualizationcpp

5.73 score 1 stars 36 scripts 328 downloads 5 mentions 9 exports 157 dependencies

Last updated 2 months agofrom:38e28ccfba. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-win-x86_64NOTENov 29 2024
R-4.5-linux-x86_64NOTENov 29 2024
R-4.4-win-x86_64NOTENov 29 2024
R-4.4-mac-x86_64NOTENov 29 2024
R-4.4-mac-aarch64NOTENov 29 2024
R-4.3-win-x86_64NOTENov 29 2024
R-4.3-mac-x86_64NOTENov 29 2024
R-4.3-mac-aarch64NOTENov 29 2024

Exports:ComputeMotifScoreComputePValuesdtMotifMatchGetIUPACSequenceLoadFastaDataLoadMotifLibraryLoadSNPDataMatchSubsequenceplotMotifMatch

Dependencies:abindade4annotateAnnotationDbiaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbrioBSgenomebslibcachemcallrcaToolsclicliprCNErcodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydescdiffobjdigestDirichletMultinomialdplyrevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2glueGO.dbgtablegtoolshighrhmshtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemotifStackmunsellnlmeopensslpillarpixmappkgbuildpkgconfigpkgloadplogrplyrpngpoweRlawpracmapraiseprettyunitsprocessxprogresspspurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownrprojrootRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesseqLogosnowspSparseArraystringistringrSummarizedExperimentsystestthatTFBSToolsTFMPvaluetibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisLitevroomwaldowithrxfunXMLxtableXVectoryamlzlibbioc

atSNP: affinity tests for regulatory SNP detection

Chandler Zuo, Sunyoung Shin, Sunduz Keles

Rendered fromatsnp-vignette.rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2021-04-26
Started: 2018-12-29

Readme and manuals

Help Manual

Help pageTopics
atSNP: affinity tests for regulatory SNP detectionatSNP-package
Compute the scores for SNP effects on motifs.ComputeMotifScore
Compute p-values for affinity scores.ComputePValues
Compute the augmented matching subsequence on SNP and reference allele s.dtMotifMatch
A motif library containing 2065 motifs downloaded from http://compbio.mit.edu/encode-motifs/motifs.txt.encode_motif
The information for the motif library downloaded from http://compbio.mit.edu/encode-motifs/motifs.txt.encode_motifinfo
Get the IUPAC sequence of a motif.GetIUPACSequence
A motif library containing 593 motifs downloaded from http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_all .txt.jaspar_motif
The information for the motif library downloaded from http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_all .txt.jaspar_motifinfo
Load the SNP data from fasta files.LoadFastaData
Load position weight matrices.LoadMotifLibrary
Load the SNP information and code the genome sequences around the SNP locations.LoadSNPData
Compute the matching subsequence.MatchSubsequence
A sample motif library.motif_library
Composit logo plotting input containing motif scores, the matching subsequences and the augmented matching subsequences on SNP and reference allelemotif_match
Scores for the sample snp data computed based on the motif data.motif_scores
Plot sequence logos of the position weight matrix of the motif and sequences of its corresponding best matching augmented subsequence on the reference and SNP allele.plotMotifMatch
Default stationary distribution for nucleotide sequences in the reference genome.prior
A data frame for SNP information.snp_tbl
A data set for SNP information.snpInfo
Default transition probability matrix for nucleotide sequences in the reference genome.transition