Package: atSNP 1.29.0

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_1.29.0.tar.gz
atSNP_1.29.0.zip(r-4.7)atSNP_1.29.0.zip(r-4.6)atSNP_1.29.0.zip(r-4.5)
atSNP_1.29.0.tgz(r-4.6-x86_64)atSNP_1.29.0.tgz(r-4.6-arm64)atSNP_1.29.0.tgz(r-4.5-x86_64)atSNP_1.29.0.tgz(r-4.5-arm64)
atSNP_1.29.0.tar.gz(r-4.7-arm64)atSNP_1.29.0.tar.gz(r-4.7-x86_64)atSNP_1.29.0.tar.gz(r-4.6-arm64)atSNP_1.29.0.tar.gz(r-4.6-x86_64)
atSNP_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
atSNP/json (API)

# 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.
snp_tbl - A data frame for SNP information.
snpInfo - A data set for SNP information.
transition - Default transition probability matrix for nucleotide sequences in the reference genome.

On BioConductor:atSNP-1.29.0(bioc 3.24)atSNP-1.28.0(bioc 3.23)

software chipseq genomeannotation motifannotation visualization cpp

6.08 score 2 stars 40 scripts 5 mentions 9 exports 132 dependencies

Last updated from:7995f08110. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	227
linux-devel-arm64	NOTE	368
linux-devel-x86_64	NOTE	456
source / vignettes	OK	330
linux-release-arm64	NOTE	372
linux-release-x86_64	NOTE	501
macos-release-arm64	NOTE	233
macos-release-x86_64	NOTE	557
macos-oldrel-arm64	NOTE	283
macos-oldrel-x86_64	NOTE	472
windows-devel	NOTE	463
windows-release	NOTE	476
windows-oldrel	NOTE	458
wasm-release	OK	202

Exports:ComputeMotifScore ComputePValues dtMotifMatch GetIUPACSequence LoadFastaData LoadMotifLibrary LoadSNPData MatchSubsequence plotMotifMatch

Dependencies:abind ade4 askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob brio BSgenome bslib cachem callr caTools cigarillo cli codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray desc diffobj digest DirichletMultinomial dplyr evaluate farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gtable gtools highr htmltools htmlwidgets httr httr2 IRanges isoband jquerylib jsonlite knitr labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime motifStack openssl otel pillar pixmap pkgbuild pkgconfig pkgload praise processx ps purrr pwalign R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl restfulr Rhtslib rjson rlang rmarkdown rprojroot Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo seqLogo snow sp SparseArray stringi stringr SummarizedExperiment sys testthat TFBSTools TFMPvalue tibble tidyr tidyselect tinytex utf8 vctrs viridisLite waldo withr xfun XML XVector yaml

atSNP: affinity tests for regulatory SNP detection

Rendered fromatsnp-vignette.rmdusingknitr::rmarkdown

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