Clustergrammer
Computational Tool
FAIR Metrics
0 evaluations
General Information
DescriptionWeb-based tool for visualizing and analyzing high-dimensional data as interactive and shareable heatmaps
Homepagehttp://amp.pharm.mssm.edu/clustergrammer/
Publications
Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data
Nicolas F. Fernandez; Gregory W. Gundersen; Adeeb Rahman; Mark L. Grimes; Klarisa Rikova; Peter Hornbeck; Avi Ma’ayan
Most tools developed to visualize hierarchically clustered heatmaps generate static images. Clustergrammer is a web-based visualization tool with interactive features such as: zooming, panning, filtering, reordering, sharing, performing enrichment analysis, and providing dynamic gene annotations. Clustergrammer can be used to generate shareable interactive visualizations by uploading a data table to a web-site, or by embedding Clustergrammer in Jupyter Notebooks. The Clustergrammer core libraries can also be used as a toolkit by developers to generate visualizations within their own applications. Clustergrammer is demonstrated using gene expression data from the cancer cell line encyclopedia (CCLE), original post-translational modification data collected from lung cancer cells lines by a mass spectrometry approach, and original cytometry by time of flight (CyTOF) single-cell proteomics data from blood. Clustergrammer enables producing interactive web based visualizations for the analysis of diverse biological data.
Metrics:
Tool Parameters(required parameters are marked in bold, optional parameters in italic)
Top GenesNumber of top genes displayed in the Clustergrammer heatmap visualization, as ranked by the ranking method.
Normalization MethodMethod used to normalize the gene expression data displayed in the Clustergrammer visualization.
Normalization AxisAxis along which the normalization has been performed.
Gene Rank MethodMetric used to rank the rows of the Clustegrammer matrix visualization.
Canned Analyses generated by the tool

Dataset Accession
Tool Name

Interactive heatmap visualization of RNA-seq dataset GSE16256
Highly interactive web-based heatmap visualization of the top 500 most variable genes in t...
Interactive heatmap visualization of RNA-seq dataset GSE17312
Highly interactive web-based heatmap visualization of the top 500 most variable genes in t...
Interactive heatmap visualization of RNA-seq dataset GSE18927
Highly interactive web-based heatmap visualization of the top 500 most variable genes in t...
Interactive heatmap visualization of RNA-seq dataset GSE22959
Highly interactive web-based heatmap visualization of the top 500 most variable genes in t...
Interactive heatmap visualization of RNA-seq dataset GSE24565
Highly interactive web-based heatmap visualization of the top 500 most variable genes in t...
Interactive heatmap visualization of RNA-seq dataset GSE26880
Highly interactive web-based heatmap visualization of the top 500 most variable genes in t...
Interactive heatmap visualization of RNA-seq dataset GSE27016
Highly interactive web-based heatmap visualization of the top 500 most variable genes in t...
Interactive heatmap visualization of RNA-seq dataset GSE27452
Highly interactive web-based heatmap visualization of the top 500 most variable genes in t...
Interactive heatmap visualization of RNA-seq dataset GSE28115
Highly interactive web-based heatmap visualization of the top 500 most variable genes in t...
Interactive heatmap visualization of RNA-seq dataset GSE29278
Highly interactive web-based heatmap visualization of the top 500 most variable genes in t...
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Datasets analyzed by the tool

Keyword
Tool Name

GSE65926
Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed
4
GSE53386
Single-cell RNA-Seq transcriptome analysis of circular RNAs in mouse embryos
4
GSE50445
IVT-seq reveals extreme bias in RNA-sequencing
3
GSE55504
Domains of genomewide gene expression dysregulation in Down syndrome [RNA-seq]
3
GSE65621
Asymmetry of STAT action in driving IL-27 and IL-6 transcriptional outputs and cytokine specificity
3
GSE74977
The LRF/ZBTB7A transcription factor is a BCL11A-independent repressor of fetal hemoglobin
2
GSE58679
Human hepatocyte metaplasia in injured humanized mouse livers
2
GSE80136
Whole transcriptome splicing analysis in isogenic lung epithelial and adenocarcinoma cell lines with or without a recurrent splicing factor mutation, ...
2
GSE54473
Transcriptionally repressive histone modifying enzymes a role in olfactory receptor expression
2
GSE86903
Comparative principles of DNA methylation reprogramming during human and mouse in vitro primordial germ cell specification [Mouse and Human RNA-seq an...
2
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