Man pages for PietaSchofield/plibb
Pieta Schofield's repository of former useful R functions

addCiteinclude citation for package in markdown
alignBWASimple subread aligner
alignStarSimple STAR aligner does everything counts junctions and...
alignSubjuncSimple subjunc aligner does everything counts junctions and...
alignSubreadSimple subread aligner
anscoreA N Spiess bigcore function
applyQDNAFilterApply QDNAseq filter
autoCommitLoop through Project code committing and pulling as necessary
bamToBedcreate bed file from a bam file
base2decConvert a bit string to a number
bigcorlarge correlation matrix with ff
buildAllBuild an Rmarkdown file or directory of files into html
CitePresPresentation citation
cnvAnnoGenesannotate CNV segmentation and copynumber call
cnvAnnoSegsannotate CNV segmentation and copynumber call
cnvCopyNumberFunction for reading in wig file from a single sample
cnvGIindexCalculate Genome Instability
cnvLogRatioFunction for reading in wig file from a pair of samples
cnvSegmentsegment as copy number data set
codeHooksimple knitr hook for code chunk referencing
collateRPGcollate a directory of STAR .ReadsPerGene.out.tab files
custHMMsegmentCustom CNV segmentation
dedupCNVrun the picard and GATK pre processing steps on bam...
delWeekgetWeek return the data for the week comencing
DSFromFCLoad Fcount output from : DEXSeq_after_Fcount.R into DEXSeq...
edtedit a file
evalCluster2evalCluster
evalSigSurvevalCluster
factorisefind divisors of an integer
filter150kbfilter150kb
genBibtexgenbibtex
genCNValignmentStatsgenerate alignments stats for BWA CNV alignments
genCNVmapGCgenerate wiggle tracks for HMMcopy
genCNVwigsgenerate wiggle tracks for HMMcopy
genCovTracksgenerate some bigwig tracks from paired reads
genPBSHeadBatch job script creation
genSGEHeadBatch job script creation
genSlurmHeadBatch job script creation
genSRstatsgenerate stats files for subread / subjunc alignments for...
getFilesget files from the cluster using scp to avoid using fuse for...
getProjectget information from project xlsx
getQCget basic stats from fastQC html
getSpikeInNormget results from nicks spike-in db
getWeekgetWeek return the data for the week comencing
goedit most recent note
hmAnalysisuse heatmap and tree cutting
knithook_plotkniter hook for figure numbering
lcklist the citation keys for a package
loadSubreadOutputLoad Fcount output from : DEXSeq_after_Fcount.R into DEXSeq...
logRunlogRun
logTimeLoad data from OfficeTime export into my time recording DB...
macOpensimple wrapper to open a file at the commandline on a mac
mergeBAMSmerge some bamfiles
multiplotMultiple plot function
newFilecreate a new notebook file
newNotecreate a new notebook file
newProjectcreate a new project
plibplib
plotCNVPlot CNV profiles
plotKMplot Kaplan Myer curves
plotSubTreeplot a dendrogram borrowed from ape zoom with ammendments
pubGoDrender the current document
publishPublish all relevant files from the local directory to my...
qstatqstat
rbrebuild a package
rcrender the current document
rcmdexecute a command remotely via ssh
readDREMEread in dreme results file
readENCODEreadENCODE read broadPeak and narrowPeak formats and return a...
readFCreadFC read a featureCount File
readGMTread in an MSigDB file with gene set
readMEMEread in meme xml results file into an R list structure
readPrismRead a Prism file.
readTRANSFACTread a transfact PWM file
retGenBankRetrieve GENBANK details
rlsFileslist remote directory
rshexecute a command remotely via ssh
runCPHrunCPH: runs cox proportional hazard models against patients...
runFastQCSubmit a list of files associated with a project for QC...
runFCRun featureCounts on a set of bam files
runHMMcopyScript for performing copy number analysis using HMMcopy
runJAFFArun JAFFA fusion gene detection
runMACS2submit a MACS2 job on the the cluster
runQSTrimSubmit a list of files associated with a project for QC...
runQualimapQC check using Qualimap
runRScriptgenerate and submit a batch job that runs an Rjob
runScriptgenerate and submit a batch job
runSICERrun SICER on a set of file pairs
runStarAlignSubmit a list of files associated with a project for bwa...
sortBAMsort a bamfile
splitBAMSa routine to split and filter by insert size strand specific...
splitStrandedBAMa routine to split and filter by insert size strand specific...
ssBAMtoBWscreate strand specific bigwigs from a standed bamfile
sswigToBigWigcreate strand specific bigwigs from a standed bamfile
strandedBamImportStranded bam import
stripPluralsrebuild a package
subFastQCSubmit a cluster job to fastQC a directory
subJobSubmit a job to the cluster
sumCNValignStatsSummarise the mapping statistics information for a specific...
sumForPlotsumForPlot
summariseQualimapgather alignment statistic on a directory of star alignments
summariseSTARgather alignment statistic on a directory of star alignments
summariseSubreadgather alignment statistic on a directory of star alignments
survAnalsurvAnal: runs cox proportional hazard models against...
survAnal2survAnal: runs cox proportional hazard models against...
survClustsurvAnal: runs cox proportional hazard models against...
survClustAnalsurvival analysis of expression profile clustered data
survFitsurvAnal: runs cox proportional hazard models against...
survFit2survAnal: runs cox proportional hazard models against...
survFit3survAnal: runs cox proportional hazard models against...
tabixFilerun tabix to produce compressed indexed file
PietaSchofield/plibb documentation built on Nov. 11, 2018, 5:15 a.m.