Man pages for zeropin/TFCookbook
Analyzing protein-DNA interactions data in principled way
| addAnchorMatrix | Add some prefixed sequence to existing energy matrix |
| as.Coefficients | Convert energy matrix to energy model coefficients Encoding... |
| as.PEM | Convert defined subject to position energy matrix |
| buildEnergyModel | Build energy model based on Sequence-Energy relationship |
| buildMethylationModel | Build model of methylation effect based on pair-wise compared... |
| composeMotif | Build composite motif based on two existing motifs with... |
| countMismatch | Count the number of mismatches of sequence(s) to some... |
| decomposeMotif | Decompose some composite motif into two separate submotifs |
| getSeqFromUCSC | Get DNA sequences from UCSC genome database directly through... |
| highlightMismatch | Highlight the mismatches of sequence(s) to some reference... |
| kmer | Enumerate all k-mer sequences |
| matchPEM | find binding sites within some GenomicRanges or DNA sequences... |
| plotEnergyLogo | Visualize some energy matrix by plotting logo |
| predictEnergy | Predict the binding energy of input sequences based on energy... |
| predictEnergyMW | Predict the binding energy of input sequences based on energy... |
| reverseComplement | Reverse some existing position energy matrix |
| selectVariants | Select sequence variants based on the max number of... |
| SeqToByte | Convert DNA sequences to binary code based on various... |
| SeqToMethylByte | Convert DNA sequences to binary code only including... |
