Man pages for mPloenzke/learnMotifs
Learn Nucleotide Motifs via Convolutions

calcActivationDifference	Calculate activation difference between classes.
calculate_offsets	Calculate offset
combo_constraint	Combination constraint to set non-negative and fix non-de...
combo_IGM_Motifs	Model callback function wrapper for learning IGMs along with...
combo_PWM_Motifs	Model callback function wrapper for learning PWMs along with...
deNovo_IGM_Motifs	Model callback function wrapper for learning IGMs.
deNovo_PWM_Motifs	Model callback function wrapper for learning PWMs.
EmptyBackground	Nucleotide sequences sampled from random background.
filter_regularizer	Sparse group lasso penalty applied to convolutional filters.
find_max_length	Find maximum motif length.
fixedMotif_constraint	Constrains weights to fixed motifs.
format_activation_motifs	Find maximally-activating sequences for motif plotting.
format_activations	Format filter activations for plotting.
format_filter_motifs	Format filters for motif plotting.
get_activations	Calculate activations.
info_constraint	Constrains filter weights within information bounds.
IUPAC2Matrix	Convert dna strings to PFM
layer_deNovo	Custom 2-D convolution wrapper with to learn IGMs or PWMs.
layer_fixedMotif	Custom 2-D convolution wrapper for fixed IGMs or PWMs
layer_topN_max_pooling	Top max-pooled hits
make_epoch_dir	Create output directory for current training epoch.
MYC_CTCF_IRF	Nucleotide sequences sampled from known motifs.
my_readHOCOMOCOMatrix	Read HOCOMOCO file in JASPAR-format.
my_readJASPARMatrix	Read JASPAR file-format.
negative_constraint	Constrains weights to be negative.
nonnegative_constraint	Constrains weights to be non-negative.
one_hot	One-hot encoding of vector of DNA nucleotide strings
one_hot_generator	One-hot encoding fit generator
one_hot_vector	One-hot encoding of DNA nucleotide string
PFMatrix	Create PFMatrix object.
pfm_to_igm	Convert PFM to IGM.
pfm_to_pwm	Convert PFM to PWM.
plot_activation_difference	Plot effect size versus activation difference.
plot_filter_activations_byClass	Plot first-layer filter activations by class.
plot_motifs	Plot filter motifs.
position_regularizer	Position-wise lasso penalty applied to convolutional filters...
processHOCOMOCOText	Read HOCOMOCO file-format line.
processJASPARText	Read JASPAR file-format line.
pwm_constraint	Constrains filter weights within position weight bounds.
restrict_to_IGM	Constrains weights to be valid information measures.
restrict_to_PWM	Constrains weights to be valid position weight measures.
setup_log_dir	Initialize output directory.
topN_max_pooling	Top max-pooled hits R6 class wrapper
total_regularizer	Total kernel regularization function wrapper.