Package: PolySTest 0.99.7

Veit Schwämmle

PolySTest: PolySTest: Detection of differentially regulated features. Combined statistical testing for data with few replicates and missing values

The complexity of high-throughput quantitative omics experiments often leads to low replicates numbers and many missing values. We implemented a new test to simultaneously consider missing values and quantitative changes, which we combined with well-performing statistical tests for high confidence detection of differentially regulated features. The package contains functions to run the test and to visualize the results.

Authors:Veit Schwämmle [aut, cre]

PolySTest_0.99.7.tar.gz
PolySTest_0.99.7.zip(r-4.5)PolySTest_0.99.7.zip(r-4.4)PolySTest_0.99.7.zip(r-4.3)
PolySTest_0.99.7.tgz(r-4.4-any)PolySTest_0.99.7.tgz(r-4.3-any)
PolySTest_0.99.7.tar.gz(r-4.5-noble)PolySTest_0.99.7.tar.gz(r-4.4-noble)
PolySTest_0.99.7.tgz(r-4.4-emscripten)PolySTest_0.99.7.tgz(r-4.3-emscripten)
PolySTest.pdf |PolySTest.html✨
PolySTest/json (API)
NEWS

Peer review:

Bug tracker:https://github.com/computproteomics/polystest/issues

On BioConductor:PolySTest-0.99.6(bioc 3.20)

massspectrometryproteomicssoftwaredifferentialexpression

28 exports 1.45 score 130 dependencies 10 scripts

Last updated 1 months agofrom:95342dad9b. Checks:OK: 1 ERROR: 6. Indexed: yes.

Exports:check_for_polystestcheck_stat_namescreate_pairwise_comparisonsFindFCandQlimFindFCandQlimAlternativeget_numthreadslimma_pairedlimma_unpairedMissingStatsMissingStatsDesignMissValPDistrperm_unpairedpermtest_pairedplotExpressionplotHeatmaplyplotPvalueDistrplotRegNumberplotUpsetplotVolcanoPolySTest_pairedPolySTest_unpairedrp_unpairedRPStatsset_mfrowStatsForPermutTestttest_pairedttest_unpairedupdate_conditions_with_lcs

Dependencies:abindaskpassassertthatbase64encBiobaseBiocGenericsbitopsbslibcacachemcallrcaToolscirclizecliclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDelayedArraydendextenddigestdplyreggevaluatefansifarverfastmapfdrtoolfontawesomeforeachfsgclusgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2GlobalOptionsgluegplotsgridExtragtablegtoolsheatmaplyhighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpermutepillarpkgconfigplotlyplyrprocessxpromisespspurrrqapqvalueR6rappdirsRColorBrewerRcppregistryreshape2rlangrmarkdownS4ArraysS4VectorssassscalesseriationshapeshinysourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexTSPUCSC.utilsUpSetRutf8vctrsveganviridisviridisLitewebshotwithrxfunxtableXVectoryamlzlibbioc