All functions
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ResizeReads()
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preprocess reads to count only 5' overlaps |
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activeChrs()
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Match BAM headers bw files and get active chromosome list (from restrict)
(written by Aaron Lun, 12 Dec 2014, copied and modified here) |
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annotateTSS()
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Annotate the provided Transcription Start Sites |
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check_capSet()
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Check capset validity |
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demultiplexFASTQ()
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Demultiplex and tag fastq files using sample barcodes |
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detectDiffTSS()
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Detect differentially expressed Transcription Start Sites between two conditions (test) |
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detectTSS()
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Detection of Trancription start sites based on local enrichment |
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exampleCSobject()
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Create example CapSet object |
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exportTSS()
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Export the detected TSS from CapSet object as .bed files |
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filterDuplicates()
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Filter PCR-duplicates from mapped files using internal UMIs |
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filterDups()
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Filter PCR-duplicates from BAM file using internal UMIs |
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fitDiffTSS()
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Detect differentially expressed Transcription Start Sites between two conditions (fit model) |
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getBamFlags()
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Get flags to read from bam |
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getChromBins()
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Get chromosome bins from BAM files |
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getChromWindows()
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Get chromosome sliding windows from BAM files |
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getGeneCounts()
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Get gene-level counts from TSS data |
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getMCparams()
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Get platform-specific multicore params |
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getNormFactors()
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Calculate normalization factors from CapSet object |
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get_newfastq()
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Get data to create new ShortReadQ object after barcode trimming |
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getranks()
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Assign feature ranks on a VariantAnnotation output |
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mapCaps()
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Map the data from 5' profiling techniques |
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newCapSet()
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Create a new CapSet object |
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numReadsInBed()
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Count the number of reads in a given GRanges |
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plotPrecision()
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Plotprecision background script |
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plotReadStats()
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Plot read statistics from the CapSet object |
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plotTSSprecision()
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Compare the precision of TSS detection between multiple samples |
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sampleInfo() `sampleInfo<-`()
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Retrieve and replace sample information of a CapSet object |
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splitBAM_byIndex()
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Split the composite BAM file using internal indexes (MAPCap) |
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splitBAM_byRepindex()
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Split the composite BAM file using replicate indexes (MAPCap data) |
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split_fastq()
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Split paired-end fastq by barcodes |
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splitranks()
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Get features with the best rank for each TSS |
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strandBinCounts()
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Perform stranded Bin counts |