The exRNA Atlas has an Application Programming Interface that can be used for programmatic access to Atlas data and metadata. More information can be found on the exRNA Atlas API Documentation page.


The exceRpt small RNA-seq analysis pipeline utilizes its own endogenous alignment and quantification engine to map and profile various small RNA libraries, including miRNAs from miRBase, tRNAs from gtRNAdb, piRNAs from piRNABank, annotations from Gencode, and circRNAs from circBase. exceRpt also allows users to map to exogenous miRNAs and rRNAs as well as a large variety of exogenous genomes (bacteria, viruses, fungi, metazoa, etc.). Abundance estimates for each of the requested libraries are given as output, as are quality control metrics such as read-length distributions, summaries of reads mapped to each library, and detailed mapping information for each read. exceRpt also supports *N random barcode identification on the inner edges (3', 5', or both) of adapter sequences. These random barcodes help normalize the read counts for amplification artifacts and serve as an alternative to the read-count for smallRNA quantitation.

Rozowsky J et al. "exceRpt: A comprehensive analytic platform for extracellular RNA profiling" Cell Syst. (2019) 8: 352-357.

exceRpt on GitHub

exceRpt Analysis Pipeline Flowchart


NanoFlow Repository

The NanoFlow Repository provides the bioinformatics infrastructure for nanoflow data, computational deconvolution methods, and informatics tools developed by NCI to complement, computationally validate, and integrate single label/antigen cytometry quantitation and single EV RNA/DNA detection methods using molecular labels. You can use the NanoFlow Repository to explore, share, and contribute nanoparticle flow cytometry experiments annotated according to the MIFlowCyt-EV standards.


Genboree is a web-based platform for multi-omic research and data analysis using the latest bioinformatics tools.

Genboree small and long RNA-seq analysis pipelines

The long RNA-Seq pipeline uses several well-established tools, including FastQC, Bowtie, Samtools, and specific modules from RSEQtools. FastQC performs a quality check on the sequence reads, Bowtie maps the reads to the reference genome, and Samtools is used to post-process the aligned reads. Downstream analysis utilizes RSEQtools modules to perform gene-expression quantification, visualize signal tracks of mapped reads, calculate mapping bias, and compute annotation coverage.

XDec (Expression Deconvolution) tool

XDec (Expression Deconvolution) is a deconvolution tool for RNA-seq expression data. Starting with complex gene expression profiles of bulk tissue or biofluid samples, one can estimate constituent cell type or cargo type composition of each input sample as well as gene transcription profiles of constituent cell/cargo types. XDec is available via

  • Genboree workbench with either private uploaded samples or publicly available exRNA Atlas samples
  • Github repo ( with one line install command for Rstudio

exRNA Data Slicer

exRNA Data Slicer extends examination of exRNA Altas samples and exRNA biology by enabling further exploration of RNA binding proteins (RBP) that carry exRNAs (exRBPs). It is used to identify exRBP binding regions in exRNAs by intersecting regions of interest (BED files) with exRNA Atlas profiles. The exRNA Data Slicer is available via


miRDaR is a web application designed to help researchers select the best RNA isolation protocol for detection and reproducibility of miRNAs of interest to them. It accompanies the publication below and replaces the earlier Protocols Decision Tree.

Srinivasan et al. "Small RNA sequencing across diverse biofluids identifies optimal methods for exRNA isolation" Cell (2019) 177: 446-462.


FunRich is a software tool used mainly for functional enrichment and interaction network analysis of genes and proteins. The results of the analysis can be depicted graphically in the form of Venn, Bar, Column, Pie and Doughnut charts. Users can identify genes and proteins from a comprehensive set of organismal genomic databases or load custom databases against which to carry out functional enrichment analysis. FunRich exists as both a web and a stand-alone Windows application, each with slightly different capabilities.


Data Use Cases

The DMRR has developed several use cases based on consortium members' datasets and publications. The purpose of these use cases is to highlight the software tools developed by the DMRR, with the goal that all future datasets generated by the consortium can be analyzed reproducibly and compared to each other.

2019 Update: See Murillo et al. for an integrative analysis of data in exRNA Atlas version 4P1. The use cases below use older versions of exceRpt and other software. They are good introductory tutorials, but please use them with caution. If you need help with a use case not covered by what you see here, please contact us at

Murillo OD et al. "exRNA Atlas analysis reveals distinct extracellular RNA cargo types and their carriers present across human biofluids" Cell (2019) 177: 463-477.

  • Use Case 1: Studying Exogenous exRNA
    • Version 3.0: Using the exRNA Atlas and exceRpt pipeline v4.6.3 (pdf, pptx, article)
    • Version 1.01: Using Genboree Workbench, and before exceRpt had automatic exogenous exRNA mapping (pdf, pptx, article)
  • Use Case 2: exRNA in Alzheimer's and Parkinson's Diseases
    • Use Case 2 Part 1: The exceRpt Pipeline (pdf, pptx, data, article)
    • Use Case 2 Part 2: The exRNA Atlas, DEseq and exceRpt pipelines, Vesiclepedia, and Pathway Analysis (pdf, data, article)
  • Use Case 3: Biomarker Potential and Limitations of Circulating miRNA (pdf, pptx, data, article)