Package: seq2pathway 1.37.0
Arjun Kinstlick
seq2pathway: a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of "seq2gene" and "gene2path" components. The seq2gene links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2pathway summarizes gene scores to pathway-scores for each sample. The seq2gene has the feasibility to assign both coding and non-exon regions to a broader range of neighboring genes than only the nearest one, thus facilitating the study of functional non-coding regions. The gene2pathway takes into account the quantity of significance for gene members within a pathway compared those outside a pathway. The output of seq2pathway is a general structure of quantitative pathway-level scores, thus allowing one to functional interpret such datasets as RNA-seq, ChIP-seq, GWAS, and derived from other next generational sequencing experiments.
Authors:
seq2pathway_1.37.0.tar.gz
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seq2pathway.pdf |seq2pathway.html✨
seq2pathway/json (API)
NEWS
| # Install 'seq2pathway' in R: |
| install.packages('seq2pathway', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- Chipseq_Peak_demo - Chip seq loci data example
- GRanges_demo - Loci information with GRanges format
- dat_RNA - RNA sequence data example
- dat_chip - Chip seq data example
On BioConductor:seq2pathway-1.37.0(bioc 3.20)seq2pathway-1.36.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:31d3c8a44b
Exports:addDescriptionFisherTest_GO_BP_MF_CCFisherTest_MsigDBgene2pathway_testplotTop10runseq2generunseq2pathway
Dependencies:AnnotationDbiaskpassbackportsbase64encBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrdigestdoParalleldplyrdynamicTreeCutevaluatefansifarverfastclusterfastmapfilelockfontawesomeforeachforeignFormulafsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2glueGO.dbgridExtraGSAgtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2imputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngpreprocessCoreprettyunitsprogresspurrrR6rappdirsRColorBrewerRcpprlangrmarkdownrpartRSQLiterstudioapiS4Vectorssassscalesseq2pathway.datastringistringrsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisviridisLiteWGCNAwithrxfunxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Retrieve "gene description" attributes for gene symbol. | addDescription |
| chip seq loci data example | Chipseq_Peak_demo |
| chip seq data example | dat_chip |
| RNA sequence data example | dat_RNA |
| A wrapper function to perform the Fisher's exact test, using GO-defined genesets. | FisherTest_GO_BP_MF_CC |
| A wrapper function to perform conditional Fisher's exact test, using custom-defined genesets. | FisherTest_MsigDB |
| A wrapper function to perform gene2pathway test. | gene2pathway_test |
| loci information with GRanges format | GRanges_demo |
| A wrapper function to plot top10 test results. | plotTop10 |
| R wrapped python function to map genomic regions on the sequence-level to genes. | runseq2gene |
| An function to perform the runseq2pathway algorithm(s). | runseq2pathway |