Software

Software

Genboree

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

Genboree Workbench Long RNA-Seq analysis pipeline

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.

exceRpt - Genboree Workbench Small RNA-seq analysis pipeline

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.

exceRpt Analysis Pipeline Flowchart

FunRich

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 long-term goal that all future datasets generated by the consortium can be analyzed reproducibly and compared to each other.

  • Use Case 1: Exogenous exRNA (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)