Package: traseR 1.37.0

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_1.37.0.tar.gz
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traseR_1.37.0.tgz(r-4.4-any)traseR_1.37.0.tgz(r-4.3-any)
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traseR.pdf |traseR.html✨
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
Tcell - Peak regions of H3K4me1 in Peripheral blood T cell
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

On BioConductor:traseR-1.37.0(bioc 3.21)traseR-1.36.0(bioc 3.20)

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 200 downloads 1 mentions 10 exports 52 dependencies

Last updated 26 days agofrom:93e91fe46c. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

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

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

Perform GWAS trait-associated SNP enrichment analyses in genomic intervals

Rendered fromtraseR.Rnwusingutils::Sweaveon Oct 31 2024.

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