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