# Identify Different Architectures of Sequence Elements

## Documentation for package ‘seqArchR’ version 1.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

collate_clusters | Collate sequence IDs from an existing clustering according to a new, given clustering of the existing clusters
collate_seqArchR_result | Collate raw clusters at the chosen iteration of seqArchR result
get_clBasVec | Get functions for seqArchR result object
get_clBasVec_k | Get functions for seqArchR result object
get_clBasVec_m | Get functions for seqArchR result object
get_one_hot_encoded_seqs | Get one-hot encoded sequences
get_seqClLab | Get functions for seqArchR result object
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
plot_arch_for_clusters | Plot cluster architectures as sequence logos.
plot_ggseqlogo_of_seqs | Plot sequence logo of a collection of sequences
prepare_data_from_FASTA | Generate one-hot encoding of sequences given as FASTA file
seqArchR | seqArchR: A package for de novo discovery of different sequence architectures
seqs_str | Get sequences from the seqArchR result object
set_config | Set seqArchR run configuration
viz_bas_vec | Visualize the NMF basis vectors
viz_pwm | Visualize a position weight matrix as a heatmap or sequence logo
viz_seqs_acgt_mat | Visualize raw DNA sequences as an image