% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/seqArchRplus.R
\docType{package}
\name{seqArchRplus}
\alias{seqArchRplus}
\title{seqArchRplus: A package for downstream analyses of promoter sequence
architectures/clusters identified by seqArchR}
\description{
This package facilitates various downstream analyses and visualizations
for clusters/architectures identified in promoter sequences. If a seqArchR
result object is available, and in addition, the CAGEr object or information
on the tag clusters, this package can be used for the following:
}
\details{
- Order the sequence architectures by the interquantile widths (IQWs) of the
tag clusters they originate from. See `CAGEr` vignette for more information.
  \code{\link{order_clusters_iqw}}

- Visualize distributions of IQW, TPM and conservation scores per cluster
  \code{\link{iqw_tpm_plots}}

- Visualize the percentage annotations of promoter sequence per cluster
  \code{\link{per_cluster_annotations}}

- Visualize heatmaps of occurrences of motifs (as words) in sequences
  \code{\link{plot_motif_heatmaps}} and \code{\link{plot_motif_heatmaps2}}

- Visualize the above plots as (publication ready) combined panels viewable
for different samples as HTML reports

- Following per cluster visualizations:

    - sequence logos of architectures (including strand-separated ones)
      \code{\link{per_cluster_seqlogos}}

    - distributions of promoters on different chromosomes/strands
      \code{\link{per_cluster_strand_dist}}

    - GO term enrichments
      \code{\link{per_cluster_go_term_enrichments}}

- Produce BED track files of seqArchR clusters for visulization in a genome
browser or IGV
  \code{\link{write_seqArchR_cluster_track_bed}}

- Curate seqArchR clusters
  \code{\link{curate_clusters}}

- (future) Generate HTML reports that help you navigate this wealth of
information with ease, and enable insights and hypotheses generation
}
\section{Functions for data preparation and manipulation}{

\itemize{
\item \code{\link{prepare_data_from_FASTA}}
\item \code{\link{get_one_hot_encoded_seqs}}
}
}

\section{Functions for visualizations}{

\itemize{
\item \code{\link{plot_arch_for_clusters}}
\item \code{\link{plot_ggseqlogo_of_seqs}}
\item \code{\link{viz_bas_vec}}
\item \code{\link{viz_seqs_acgt_mat}}
\item \code{\link{viz_pwm}}
}
}

\author{
Sarvesh Nikumbh
}
