Main functions

Most basic functions

seqArchR()

seqArchR: A package for de novo discovery of different sequence architectures

set_config()

Set seqArchR run configuration

Prepare input

Functions enabling preparation of input

prepare_data_from_FASTA()

Generate one-hot encoding of sequences given as FASTA file

get_one_hot_encoded_seqs()

Get one-hot encoded sequences

Getter functions

Getter functions for seqArchR result object

get_clBasVec() get_clBasVec_k() get_clBasVec_m() get_seqClLab()

Get functions for seqArchR result object

seqs_str()

Get sequences from the seqArchR result object

Visualization functions

Functions enabling visualization of intermediate and final output

plot_arch_for_clusters()

Plot cluster architectures as sequence logos.

plot_ggseqlogo_of_seqs()

Plot sequence logo of a collection of sequences

viz_pwm()

Visualize a position weight matrix as a heatmap or sequence logo

viz_bas_vec()

Visualize the NMF basis vectors

viz_seqs_acgt_mat()

Visualize raw DNA sequences as an image

Manipulate seqArchR result

Functions to manipulate elements from seqArchR result

collate_seqArchR_result()

Collate raw clusters at the chosen iteration of seqArchR result

collate_clusters()

Collate sequence IDs from an existing clustering according to a new, given clustering of the existing clusters

get_seqs_clust_list()

Retrieve sequence clusters as a list from the sequence labels

make_PWMs()

Make a PWM-resembling matrix out of a given n-vector