Files in mskilab/skitools

Various mskilab R utilties

DESCRIPTION

NAMESPACE

NEWS.md R/skitools.R

R/skitools.txt

README.md

inst/extdata/snpeff_ontology.rds

install_bioc.sh

man/PPplots.Rd man/af.Rd man/af2.Rd man/affine-map-methods.Rd man/alignment_metrics.Rd man/all.paths.Rd man/allele_multiplicity.Rd man/alpha.Rd man/anno.hops.Rd man/arrstring.Rd man/bisort.Rd man/blend.Rd man/border.Rd man/bplot.Rd man/brew.Rd man/brewer.master.Rd man/bsub_cmd.Rd man/bubblemap.Rd man/camerplot.Rd man/capitalize.Rd man/cc.Rd man/ccf.Rd man/charToDec.Rd man/chr2num.Rd man/chron.Rd man/chunk.Rd man/circos.Rd man/clock.Rd man/clone_cluster.Rd man/col.scale.Rd man/col.slice.Rd man/collapse.paths.Rd man/contig.support.Rd man/cumseg.Rd man/d3igraph.Rd man/dcast2.Rd man/dd.Rd man/ddd.Rd man/dedup.Rd man/dev.all.off.Rd man/dflm.Rd man/dfstring.Rd man/dirr.Rd man/discordant.pairs.Rd man/dmix.Rd man/dodo.call.Rd man/dot-e2class.Rd man/dplot.Rd man/dtgr.Rd man/dtt.Rd man/du.Rd man/dunlist.Rd man/edge2tip.Rd man/elcycles.Rd man/file.dir.Rd man/file.name.Rd man/file.ready.Rd man/fill.blanks.Rd man/fisher.combined.Rd man/fisher.pairwise.Rd man/fisher.plot.Rd man/flow_slurm_status.Rd man/fready.Rd man/fuckr.Rd man/func_code.Rd man/gatk_callvariants.Rd man/gatk_haplotypecaller.Rd man/gatk_oncotate.Rd man/gc_content.Rd man/get.pileup.gtrack.Rd man/get.var.col.Rd man/get_dryclean_pon_path.Rd man/get_dryclean_pon_template.Rd man/get_gene_ampdels_from_jabba.Rd man/get_gene_copy_numbers.Rd man/ggjs.Rd man/gigs.Rd man/gr.all.Rd man/gr.breaks.Rd man/gr.eval.Rd man/gr.isclip.Rd man/gr.isdisc.Rd man/gr.mincov.Rd man/gr.pad.Rd man/gr.peaks.Rd man/gr.readfilter.Rd man/gr.refactor.Rd man/gr.round.Rd man/gr.tostring.Rd man/gr2gatk.Rd man/gr2grl.Rd man/gr2json.Rd man/grl.filter.Rd man/grl.span.Rd man/grl.split.Rd man/grok_bcf.Rd man/grok_vcf.Rd man/gsea_leading_edge.Rd man/gstring.Rd man/headf.Rd man/hets.Rd man/html_link.Rd man/html_tag.Rd man/igv.Rd man/igv.loci.Rd man/igv_host.Rd man/img.html.Rd man/img_link.Rd man/import.ucsc.Rd man/ind2sub.Rd man/install.packages.bioc.Rd man/install.packages.github.Rd man/internal.Rd man/is.dup.Rd man/jhom.Rd man/junction.support.Rd man/karyoSim.Rd man/kill.zombies.Rd man/label.runs.Rd man/ldim.Rd man/levapply.Rd man/lighten.Rd man/list.expr.Rd man/loud.Rd man/lsos.Rd man/maf2vcf.Rd man/maf_classify.Rd man/maf_coding.Rd man/maf_disp.Rd man/maf_exonic.Rd man/maf_genic.Rd man/maf_indel.Rd man/maf_nonyn.Rd man/maf_ns.Rd man/maf_sub.Rd man/maf_syn.Rd man/maf_to_simple.Rd man/maf_truncating.Rd man/maflite.Rd man/match.bs.Rd man/match.seq.Rd man/memu.Rd man/mmatch.Rd man/modix.Rd man/morder.Rd man/more.Rd man/mski_alpha.Rd man/mtable.Rd man/muffle.Rd man/multicoco.Rd man/munlist.Rd man/mut_genecluster.Rd man/mutclusters.Rd man/mutpairsd.Rd man/mutrate_window.Rd man/nnnusvr.Rd man/nona.Rd man/nz.Rd man/oncoprint.Rd man/oncotable.Rd man/oneoffs.Rd man/padding.Rd man/parsesnpeff.Rd man/phist.Rd man/pindel.Rd man/plop.Rd man/plot.blank.Rd man/plot_multiplicity.Rd man/pmGSEA.Rd man/pp2gb.Rd man/ppdf.Rd man/ppgrid.Rd man/ppng.Rd man/preprocess_cov_for_dryclean.Rd man/print_eq.Rd man/process_gencode.Rd man/pscatter.Rd man/qhost.Rd man/qq_pval.Rd man/qq_repel.Rd man/qstat.Rd man/query_lsf_out.Rd man/queues.Rd man/quickSig.Rd man/qviz.Rd man/ra.overlaps.Rd man/ra.union.Rd man/ra_breaks.Rd man/read.delim.cat.Rd man/readRDA.Rd man/read_hg.Rd man/read_pon_dict.Rd man/reads.to.walks.Rd man/rel2abs.Rd man/relib.Rd man/reorder_maf.Rd man/rmix.Rd man/row.slice.Rd man/rpipe.Rd man/rr.Rd man/rrbind.Rd man/rrbind2.Rd man/sc.context.Rd man/score.walks.Rd man/seconds.Rd man/seqinfo2gr.Rd man/set.comp.Rd man/setxor.Rd man/sgrep.Rd man/sgrepl.Rd man/slurm_dt.Rd man/sortable.Rd man/sparse_subset.Rd man/splot.Rd man/spmelt.Rd man/ssegment.Rd man/sstat.Rd man/standardize_segs.Rd man/stavePDF.Rd man/staveRDS.Rd man/strsplit.fwf.Rd man/strsplit2.Rd man/sub2ind.Rd man/system.call.Rd man/tabstring.Rd man/tailf.Rd man/timestamp.Rd man/toggle_grfo.Rd man/ucount.Rd man/vaggregate.Rd man/variants.Rd man/vplot.Rd man/wfplot.Rd man/which.char.Rd man/wij.Rd man/wijj.Rd man/write.htab.Rd man/write.tab.Rd man/write_ggjs.Rd

skitools.Rproj

skitools.pdf tests/testthat.R tests/testthat/test_skitools.R

mskilab/skitools documentation built on July 5, 2024, 7:27 a.m.