| addCite | include citation for package in markdown |
| alignBWA | Simple subread aligner |
| alignStar | Simple STAR aligner does everything counts junctions and... |
| alignSubjunc | Simple subjunc aligner does everything counts junctions and... |
| alignSubread | Simple subread aligner |
| anscore | A N Spiess bigcore function |
| applyQDNAFilter | Apply QDNAseq filter |
| autoCommit | Loop through Project code committing and pulling as necessary |
| bamToBed | create bed file from a bam file |
| base2dec | Convert a bit string to a number |
| bigcor | large correlation matrix with ff |
| buildAll | Build an Rmarkdown file or directory of files into html |
| CitePres | Presentation citation |
| cnvAnnoGenes | annotate CNV segmentation and copynumber call |
| cnvAnnoSegs | annotate CNV segmentation and copynumber call |
| cnvCopyNumber | Function for reading in wig file from a single sample |
| cnvGIindex | Calculate Genome Instability |
| cnvLogRatio | Function for reading in wig file from a pair of samples |
| cnvSegment | segment as copy number data set |
| codeHook | simple knitr hook for code chunk referencing |
| collateRPG | collate a directory of STAR .ReadsPerGene.out.tab files |
| custHMMsegment | Custom CNV segmentation |
| dedupCNV | run the picard and GATK pre processing steps on bam... |
| delWeek | getWeek return the data for the week comencing |
| DSFromFC | Load Fcount output from : DEXSeq_after_Fcount.R into DEXSeq... |
| edt | edit a file |
| evalCluster2 | evalCluster |
| evalSigSurv | evalCluster |
| factorise | find divisors of an integer |
| filter150kb | filter150kb |
| genBibtex | genbibtex |
| genCNValignmentStats | generate alignments stats for BWA CNV alignments |
| genCNVmapGC | generate wiggle tracks for HMMcopy |
| genCNVwigs | generate wiggle tracks for HMMcopy |
| genCovTracks | generate some bigwig tracks from paired reads |
| genPBSHead | Batch job script creation |
| genSGEHead | Batch job script creation |
| genSlurmHead | Batch job script creation |
| genSRstats | generate stats files for subread / subjunc alignments for... |
| getFiles | get files from the cluster using scp to avoid using fuse for... |
| getProject | get information from project xlsx |
| getQC | get basic stats from fastQC html |
| getSpikeInNorm | get results from nicks spike-in db |
| getWeek | getWeek return the data for the week comencing |
| go | edit most recent note |
| hmAnalysis | use heatmap and tree cutting |
| knithook_plot | kniter hook for figure numbering |
| lck | list the citation keys for a package |
| loadSubreadOutput | Load Fcount output from : DEXSeq_after_Fcount.R into DEXSeq... |
| logRun | logRun |
| logTime | Load data from OfficeTime export into my time recording DB... |
| macOpen | simple wrapper to open a file at the commandline on a mac |
| mergeBAMS | merge some bamfiles |
| multiplot | Multiple plot function |
| newFile | create a new notebook file |
| newNote | create a new notebook file |
| newProject | create a new project |
| plib | plib |
| plotCNV | Plot CNV profiles |
| plotKM | plot Kaplan Myer curves |
| plotSubTree | plot a dendrogram borrowed from ape zoom with ammendments |
| pubGoD | render the current document |
| publish | Publish all relevant files from the local directory to my... |
| qstat | qstat |
| rb | rebuild a package |
| rc | render the current document |
| rcmd | execute a command remotely via ssh |
| readDREME | read in dreme results file |
| readENCODE | readENCODE read broadPeak and narrowPeak formats and return a... |
| readFC | readFC read a featureCount File |
| readGMT | read in an MSigDB file with gene set |
| readMEME | read in meme xml results file into an R list structure |
| readPrism | Read a Prism file. |
| readTRANSFACT | read a transfact PWM file |
| retGenBank | Retrieve GENBANK details |
| rlsFiles | list remote directory |
| rsh | execute a command remotely via ssh |
| runCPH | runCPH: runs cox proportional hazard models against patients... |
| runFastQC | Submit a list of files associated with a project for QC... |
| runFC | Run featureCounts on a set of bam files |
| runHMMcopy | Script for performing copy number analysis using HMMcopy |
| runJAFFA | run JAFFA fusion gene detection |
| runMACS2 | submit a MACS2 job on the the cluster |
| runQSTrim | Submit a list of files associated with a project for QC... |
| runQualimap | QC check using Qualimap |
| runRScript | generate and submit a batch job that runs an Rjob |
| runScript | generate and submit a batch job |
| runSICER | run SICER on a set of file pairs |
| runStarAlign | Submit a list of files associated with a project for bwa... |
| sortBAM | sort a bamfile |
| splitBAMS | a routine to split and filter by insert size strand specific... |
| splitStrandedBAM | a routine to split and filter by insert size strand specific... |
| ssBAMtoBWs | create strand specific bigwigs from a standed bamfile |
| sswigToBigWig | create strand specific bigwigs from a standed bamfile |
| strandedBamImport | Stranded bam import |
| stripPlurals | rebuild a package |
| subFastQC | Submit a cluster job to fastQC a directory |
| subJob | Submit a job to the cluster |
| sumCNValignStats | Summarise the mapping statistics information for a specific... |
| sumForPlot | sumForPlot |
| summariseQualimap | gather alignment statistic on a directory of star alignments |
| summariseSTAR | gather alignment statistic on a directory of star alignments |
| summariseSubread | gather alignment statistic on a directory of star alignments |
| survAnal | survAnal: runs cox proportional hazard models against... |
| survAnal2 | survAnal: runs cox proportional hazard models against... |
| survClust | survAnal: runs cox proportional hazard models against... |
| survClustAnal | survival analysis of expression profile clustered data |
| survFit | survAnal: runs cox proportional hazard models against... |
| survFit2 | survAnal: runs cox proportional hazard models against... |
| survFit3 | survAnal: runs cox proportional hazard models against... |
| tabixFile | run tabix to produce compressed indexed file |
