Identify Different Architectures of Sequence Elements

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Documentation for package ‘seqArchR’ version 1.6.0

• 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