Package: seeker 1.1.6

Jake Hughey

seeker: Simplified Fetching and Processing of Microarray and RNA-Seq Data

Wrapper around various existing tools and command-line interfaces, providing a standard interface, simple parallelization, and detailed logging. For microarray data, maps probe sets to standard gene IDs, building on 'GEOquery' Davis and Meltzer (2007) <doi:10.1093/bioinformatics/btm254>, 'ArrayExpress' Kauffmann et al. (2009) <doi:10.1093/bioinformatics/btp354>, Robust multi-array average 'RMA' Irizarry et al. (2003) <doi:10.1093/biostatistics/4.2.249>, and 'BrainArray' Dai et al. (2005) <doi:10.1093/nar/gni179>. For RNA-seq data, fetches metadata and raw reads from National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), performs standard adapter and quality trimming using 'TrimGalore' Krueger <https://github.com/FelixKrueger/TrimGalore>, performs quality control checks using 'FastQC' Andrews <https://github.com/s-andrews/FastQC>, quantifies transcript abundances using 'salmon' Patro et al. (2017) <doi:10.1038/nmeth.4197> and potentially 'refgenie' Stolarczyk et al. (2020) <doi:10.1093/gigascience/giz149>, aggregates the results using 'MultiQC' Ewels et al. (2016) <doi:10.1093/bioinformatics/btw354>, maps transcripts to genes using 'biomaRt' Durinkck et al. (2009) <doi:10.1038/nprot.2009.97>, and summarizes transcript-level quantifications for gene-level analyses using 'tximport' Soneson et al. (2015) <doi:10.12688/f1000research.7563.2>.

Authors:Jake Hughey [aut, cre], Josh Schoenbachler [aut]

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seeker.pdf |seeker.html✨
seeker/json (API)

Peer review:

Bug tracker:https://github.com/hugheylab/seeker/issues

On CRAN:

16 exports 3 stars 1.41 score 107 dependencies 1 scripts 354 downloads

Last updated 22 days agofrom:ec636b2d55. Checks:OK: 7. Indexed: yes.

Exports:checkDefaultCommandsfastqcfastqscreenfetchfetchMetadatagetPlatformsgetSalmonMetadatagetTx2geneinstallCustomCdfPackagesinstallSysDepsmultiqcsalmonseekerseekerArraytrimgaloretximport

Dependencies:abindaffyaffyioAnnotationDbiaskpassbackportsBHBiobaseBiocFileCacheBiocGenericsBiocManagerbiomaRtBiostringsbitbit64bitopsblobcachemcheckmateclicliprcodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdplyrfansifastmapfilelockforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGEOquerygluehmshttrhttr2IRangesiteratorsjsonliteKEGGRESTlatticelifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngpreprocessCoreprettyunitsprogresspurrrqsR.methodsS3R.ooR.utilsR6RApiSerializerappdirsRcppRcppParallelRCurlreadrrentrezrlangRSQLitervestS4ArraysS4VectorsselectrsessioninfoSparseArraystatmodstringfishstringistringrSummarizedExperimentsystibbletidyrtidyselecttximporttzdbUCSC.utilsutf8vctrsvroomwithrXMLxml2XVectoryamlzlibbioc