Our package relies on the following R packages to deliver its features. These dependencies play a crucial role in data processing, analysis, and visualization. We thank the developers for their invaluable contributions.
Seurat is an R toolkit
for quality control, analysis, and exploration of single cell RNA
sequencing data. ‘Seurat’ aims to enable users to identify and interpret
sources of heterogeneity from single cell transcriptomic measurements,
and to integrate diverse types of single cell data.
Signac is an R toolkit
that extends Seurat for the analysis, interpretation, and exploration of
single-cell chromatin datasets.
ChIPseeker
implements functions to retrieve the nearest genes around the peak,
annotate genomic region of the peak, statstical methods for estimate the
significance of overlap among ChIP peak data sets, and incorporate GEO
database for user to compare the own dataset with those deposited in
database. The comparison can be used to infer cooperative regulation and
thus can be used to generate hypotheses. Several visualization functions
are implemented to summarize the coverage of the peak experiment,
average profile and heatmap of peaks binding to TSS regions, genomic
annotation, distance to TSS, and overlap of peaks or genes.
GenomicRanges
is an R package that defines general-purpose containers for storing and
manipulating genomic intervals and variables along a genome. It plays a
central role in analyzing high-throughput sequencing (NGS) data. The
package provides efficient tools for handling genomic annotations and
alignments. More specialized containers for short alignments against a
reference genome and matrix-like summarization of experiments are
provided by the GenomicAlignments and SummarizedExperiment packages,
respectively, both of which build on the GenomicRanges
org.Hs.eg.db
is an R package providing Genome wide annotation for Human, primarily
based on mapping using Entrez Gene identifiers.
OmicCircos
is an R application and package for generating high-quality circular
plots for omics data.
GeneSummary
is an R package providing long description of genes collected from the
RefSeq database. The text in “COMMENT” section started with “Summary” is
extracted as the description of the gene. The long text descriptions can
be used for analysis such as text mining.
pheatmap
is an R package that provides an implementation of heatmaps, offering
greater control over the dimensions and appearance of the plot. It
allows for fine-tuning of aspects such as clustering, color schemes, row
and column annotations, and legend placement, making it highly
customizable for visualizing complex datasets.
TxDb.Hsapiens.UCSC.hg38.knownGene
is an R package Exposing an annotation databases generated from UCSC by
exposing these as TxDb objects
IRanges
is an R packages Providing efficient low-level and highly reusable S4
classes for storing, manipulating and aggregating over annotated ranges
of integers. Implements an algebra of range operations, including
efficient algorithms for finding overlaps and nearest neighbors. Defines
efficient list-like classes for storing, transforming and aggregating
large grouped data, i.e., collections of atomic vectors and DataFrames.
ggpubr is an R
package providing some easy-to-use functions for creating and
customizing ‘ggplot2’- based publication ready plots.
ggtree
is an R package designed for visualization and annotation of
phylogenetic trees and other tree-like structures with their annotation
data.
igraph
is an R package designed for simple graph and network analysis. It can
efficiently handle large graphs and provides a wide range of functions
for generating random and regular graphs, visualizing graphs, and
calculating centrality measures, among other network analysis tasks. The
package is highly versatile and widely used in fields like social
network analysis, biology, and computer science.
AMULET is a count
based method for detecting multiplets from single nucleus ATAC-seq
(snATAC-seq) data.
Samtools is a
command-line tool for processing high-throughput sequencing data,
specifically designed for manipulating SAM and BAM files. Its main
functions include file operations, data querying, quality control, and
other specific features.
Bedtools is a set of command-line tools for processing and analyzing genomic interval data, specifically designed for handling BED, GFF/GTF, and VCF files. Its main functions include interval operations, data annotation, format conversion, and other advanced analyses.