scRNAseqApp - A single-cell RNAseq Shiny app-package
The scRNAseqApp is a Shiny app package designed for interactive visualization of single-cell data. It is an enhanced version derived from the ShinyCell, repackaged to accommodate multiple datasets. The app enables users to visualize data containing various types of information simultaneously, facilitating comprehensive analysis. Additionally, it includes a user management system to regulate database accessibility for different users.
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visualizationsinglecellrnaseqinteractive-visualizationsmultiple-usersshiny-appssingle-cell-rna-seq
5.97 score 6 stars 5 scripts 375 downloadsenhancerHomologSearch - Identification of putative mammalian orthologs to given enhancer
Get ENCODE data of enhancer region via H3K4me1 peaks and search homolog regions for given sequences. The candidates of enhancer homolog regions can be filtered by distance to target TSS. The top candidates from human and mouse will be aligned to each other and then exported as multiple alignments with given enhancer.
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sequencinggeneregulationalignmentcpp
4.88 score 2 scripts 303 downloadshicVennDiagram - Venn Diagram for genomic interaction data
A package to generate high-resolution Venn and Upset plots for genomic interaction data from HiC, ChIA-PET, HiChIP, PLAC-Seq, Hi-TrAC, HiCAR and etc. The package generates plots specifically crafted to eliminate the deceptive visual representation caused by the counts method.
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dna3dstructurehicvisualization
4.72 score 13 scriptsGenomicInteractionNodes - A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data
The GenomicInteractionNodes package can import interactions from bedpe file and define the interaction nodes, the genomic interaction sites with multiple interaction loops. The interaction nodes is a binding platform regulates one or multiple genes. The detected interaction nodes will be annotated for downstream validation.
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hicsequencingsoftware
4.65 score 3 scripts 292 downloadsATACseqTFEA - Transcription Factor Enrichment Analysis for ATAC-seq
Assay for Transpose-Accessible Chromatin using sequencing (ATAC-seq) is a technique to assess genome-wide chromatin accessibility by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. ATACseqTFEA is an improvement of the current computational method that detects differential activity of transcription factors (TFs). ATACseqTFEA not only uses the difference of open region information, but also (or emphasizes) the difference of TFs footprints (cutting sites or insertion sites). ATACseqTFEA provides an easy, rigorous way to broadly assess TF activity changes between two conditions.
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sequencingdnaseqatacseqmnaseseqgeneregulation
4.60 score 1 stars 8 scripts 319 downloadsannoLinker - Annotating genomic regions through chromatin interaction links
Fast annotation of genomic peaks using DNA interaction data by constructing interaction networks with igraph, where peaks overlapping any node in a connected subgraph are annotated with all genes in that subgraph. The annotation evidence could be visualized as either a network graph or a genomic track integrated with gene annotation information.
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networkannotationvisualization
4.48 scoreGOfan - Sunburst Plot for Enriched Gene Ontology Terms
GOfan provides an intuitive and compact visualization of Gene Ontology (GO) enrichment results using a sunburst layout inspired by SynGO, preserving hierarchical relationships among GO terms and allowing color-based encoding of information such as p-values or gene counts. By converting complex GO DAGs into clean, circular representations, it allows researchers to quickly grasp the hierarchical structure and biological significance of enriched terms. The interactive and customizable visualizations facilitate exploration of key GO categories, enhancing interpretation and presentation of enrichment analyses.
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visualizationgoannotation
4.40 score 1 stars 1 scripts 193 downloads