Package: traseR 1.43.0

li chen

traseR: GWAS trait-associated SNP enrichment analyses in genomic intervals

traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.

Authors:Li Chen, Zhaohui S.Qin

traseR_1.43.0.tar.gz
traseR_1.43.0.zip(r-4.7)traseR_1.43.0.zip(r-4.6)traseR_1.43.0.zip(r-4.5)
traseR_1.43.0.tgz(r-4.6-any)traseR_1.43.0.tgz(r-4.5-any)
traseR_1.43.0.tar.gz(r-4.7-any)traseR_1.43.0.tar.gz(r-4.6-any)
traseR_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
traseR/json (API)

# Install 'traseR' in R:

install.packages('traseR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

CEU - Sampled SNPs from all SNPs of CEU population in 1000 genome project
taSNP - Trait-associated SNPs in dbGaP and NHGRI downloaded from Association Results Browser
taSNPLD - Linkage disequilibrium (>0.8) within 100kb SNPs of all trait-associated SNPs from dbGaP and NHGRI
Tcell - Peak regions of H3K4me1 in Peripheral blood T cell

On BioConductor:traseR-1.43.0(bioc 3.24)traseR-1.42.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

genetics sequencing coverage alignment qualitycontrol dataimport

3.30 score 3 scripts 1 mentions 10 exports 51 dependencies

Last updated from:086923e997. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	230
linux-devel-x86_64	NOTE	409
source / vignettes	OK	308
linux-release-x86_64	NOTE	387
macos-release-arm64	NOTE	286
macos-oldrel-arm64	NOTE	227
windows-devel	NOTE	749
windows-release	NOTE	722
windows-oldrel	NOTE	728
wasm-release	OK	188

Exports:plotContext plotGene plotInterval plotPvalue plotSNP print.traseR queryGene queryKeyword querySNP traseR

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome BSgenome.Hsapiens.UCSC.hg19 cigarillo codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options generics GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 RCurl restfulr Rhtslib rjson Rsamtools rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys XML XVector yaml

Perform GWAS trait-associated SNP enrichment analyses in genomic intervals

Rendered fromtraseR.Rnwusingutils::Sweave

Last update: 2015-11-20
Started: 2015-07-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
GWAS trait-associated SNP enrichment analyses in genomic intervals	traseR-package
Sampled SNPs from all SNPs of CEU population in 1000 genome project	CEU
Visualize of trait-associated SNPs	plotContext plotGene plotInterval plotPvalue plotSNP
Print the outcome of taSNP enrichment analyses	print.traseR
Retrieve trait-associated SNPs based	queryGene queryKeyword querySNP
trait-associated SNPs in dbGaP and NHGRI downloaded from Association Results Browser	taSNP
linkage disequilibrium (>0.8) within 100kb SNPs of all trait-associated SNPs from dbGaP and NHGRI	taSNPLD
Peak regions of H3K4me1 in Peripheral blood T cell	Tcell
TRait-Associated SNP EnRichment analyses	traseR