Package: atSNP 1.21.0

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_1.21.0.tar.gz
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atSNP_1.21.0.tar.gz(r-4.5-noble)atSNP_1.21.0.tar.gz(r-4.4-noble)
atSNP_1.21.0.tgz(r-4.4-emscripten)atSNP_1.21.0.tgz(r-4.3-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'))

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-1.21.0(bioc 3.20)atSNP-1.20.0(bioc 3.19)

bioconductor-package

9 exports 0.71 score 158 dependencies 5 mentions

Last updated 2 months agofrom:777233ae64

Exports:ComputeMotifScore ComputePValues dtMotifMatch GetIUPACSequence LoadFastaData LoadMotifLibrary LoadSNPData MatchSubsequence plotMotifMatch

Dependencies:abind ade4 annotate AnnotationDbi askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob brio BSgenome bslib cachem callr caTools cli clipr CNEr codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray desc diffobj digest DirichletMultinomial dplyr evaluate fansi farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue GO.db gtable gtools highr hms htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime motifStack munsell nlme openssl pillar pixmap pkgbuild pkgconfig pkgload plogr plyr png poweRlaw pracma praise prettyunits processx progress ps purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl readr rematch2 reshape2 restfulr Rhtslib rjson rlang rmarkdown rprojroot Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales seqLogo snow sp SparseArray stringi stringr SummarizedExperiment sys testthat TFBSTools TFMPvalue tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridisLite vroom waldo withr xfun XML xtable XVector yaml zlibbioc

atSNP: affinity tests for regulatory SNP detection

Chandler Zuo, Sunyoung Shin, Sunduz Keles

Rendered fromatsnp-vignette.rmdusingknitr::rmarkdownon Jun 30 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
atSNP: affinity tests for regulatory SNP detection	atSNP-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 allele	motif_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