FunGenPipe: Functional genomics functions and pipes

In peterjuv/FunGenPipe: Tools for building function genomics pipelines

Description

Tools for building function genomics pipelines

Genomics functions that operate with ranges and sequences

dechiperMeltDNAtime

Tagets meta-data

Functions for manipulating colors in targets. getColPats - depricated getColPats2

Plot distributions, heatmap, PCA & MDS using targets meta-data

Note: the order od data columns should (always) be kept in the order of targets. plotDistrTargets2 pheatmapTargets2 plotPCAtargets2 plotPCAtargets - depricated plotMDStargets2 plotMDStargets2_MASS - depricated

Plot distributions using limma-style data

plotDistr_RGList boxplotRLE

DEG

annotations, expression (from KBlag_doxy_Cla.R via Osijek_HFHSD.R for EKocar_fibIT.R) annotate_SEcollapsed writeExprsGEO

DEG & GSEA

write (finalized for EKocar_fibIT.R)) getWriteHeatmap_probesTTcontrasts getWriteHeatmap_probesTTcomparisons getWriteHeatmap_PgseaTTcontrasts getWriteHeatmap_PgseaTTcomparisons

GSEA

annotations & analysis getAnnKeggEntrez gscKeggEntrez annTFbyFA - depricated, replaced by getAnnTransfac getAnnTransfacEntrez gscTransfacEntrez

Author(s)

Peter Juvan, [e-mail]

peterjuv/FunGenPipe documentation built on June 18, 2021, 3:38 a.m.