Man pages for matthuska/tRap
A biophysical model for transcription factor binding affinities
| affinity | compute transcription factor binding site affinity |
| evaluate.ranking | Evaluate Ranking |
| exactgevparams | Precalculated generalized extreme value distribution... |
| fit.gev | Fit a gev distribution for a pwm matrix. |
| get.affinity.cutoff | determine significance threshold for tRap affinities |
| gevparams | parameters for the fitted extreme value distributions for... |
| jaspar | The JASPAR transcription factor database in the format... |
| local.paffinity | Calculate local p-values |
| normalize.pwm | normalize a PWM |
| paffinity | compute p-values for affinity values |
| R_affinity_multi | Calculate the TRAP affinity for each position along one or... |
| R_affinity_sum_multi | Calculate the TRAP affinity for one or more sequences (one... |
| rank.factors | Rank transcription factors according to changes in binding... |
| read.jaspar | read a jaspar matrix |
| read.pscm | read a PSCM |
| read.transfac | read a transfac matrix |
| read.transfac.dir | read a directory of transfac matrices |
| scan.sequence | identify TFBS hits in the sequence(s) |
| tRap-package | compute transcription factor binding site affinity |
