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| nucleR-package | Nucleosome positioning package for R |
| .fftRegion | FFT Region |
| .getThreshold | Threshold getter |
| .loadFiles | File loader Higher order function to import BAM or Bowtie files. Deals with wether type is 'single' or 'paired' and with the number of input files |
| .loadPairedBam | Load a paired-end-end BAM |
| .loadSingleBam | Load a single-end BAM |
| .mid | Find midpoints |
| .processStrand | Process a given strand from a BAM file to read |
| .unlist_as_integer | Unlist an IRanges object into a vector |
| .vectorizedAll | Vectorized version of 'all' |
| .xlapply | mclapply warapper |
| controlCorrection | Correct experimental profiles with control sample |
| controlCorrection-method | Correct experimental profiles with control sample |
| coverage.rpm | Coverage calculation and normalization to reads per million (rpm) |
| coverage.rpm-method | Coverage calculation and normalization to reads per million (rpm) |
| export.bed | Export ranges in BED format |
| export.bed-method | Export ranges in BED format |
| export.wig | Export values in WIG format |
| filterFFT | Clean noise and smoothing for genomic data using Fourier-analysis |
| filterFFT-method | Clean noise and smoothing for genomic data using Fourier-analysis |
| fragmentLenDetect | Fragments length detection from single-end sequencing samples |
| fragmentLenDetect-method | Fragments length detection from single-end sequencing samples |
| mergeCalls | Automatic merging of overlapped nucleosome calls |
| mergeCalls-method | Automatic merging of overlapped nucleosome calls |
| nucleosome_htseq | Example reads from high-troughtput sequencing nucleosome positioning experiment |
| nucleosome_tiling | Example intensities from Tiling Microarray nucleosome positioning experiment |
| nucleR | Nucleosome positioning package for R |
| pcKeepCompDetect | Auto detection of a fitted 'pcKeepComp' param for filterFFT function |
| peakDetection | Detect peaks (local maximum) from values series |
| peakDetection-method | Detect peaks (local maximum) from values series |
| peakScoring | Peak scoring function |
| peakScoring-method | Peak scoring function |
| plotPeaks | Nucleosome calling plot function |
| plotPeaks-method | Nucleosome calling plot function |
| processReads | Process reads from High-Troughtput Sequencing experiments |
| processReads-method | Process reads from High-Troughtput Sequencing experiments |
| processTilingArray | Obtain and clean nucleosome positioning data from tiling array |
| readBAM | Import reads from a list of BAM files. |
| readBowtie | Import reads from a vector of Bowtie files |
| syntheticNucMap | Generates a synthetic nucleosome map |