About Us

RiboSeq.Org is a platform for sharing and analyzing ribosome profiling data. Our goal is to provide a user-friendly interface for exploring publicly available ribosome profiling datasets and facilitating data-driven discoveries in the field of translation regulation.

Current Development Team

Past Developers/Current Advisors

Contact Us

If you have any questions or feedback, please email us at riboseq@gmail.com.

Workflow Details

Controlled Vocabularies

To examine the controlled vocabularies used in RDPs Metadata Cleaning please see:

Vocabularies

Reference Genomes

To find which genome and annotation was used to process the for a given species please see:

References

Tool Versions

To find which version of each tool was utilised in data processing please see:

Versions

Sample Column Descriptions

Metadata fields found in the RiboSeq Data Portal Samples Pageare explained below:

  • Run Accession: The unique run identifier for the dataset.
  • Study Accession: The BioProject Accession from which this run originated.
  • Organism: The species of the organism from which the data was generated.
  • Library Type: The library type of this run inferred from metadata
  • Inhibitor: The inhibitor used to stall ribosomes in the Ribo-Seq protocol of this run.
  • Cell Line: The cell line used in the Ribo-Seq protocol of this run.
  • Sex: The inferred sex of the sample

Study Column Descriptions

Metadata fields found in the RiboSeq Data Portal Studies Page are explained below:

  • Name: Study Name assigned to this BioProject. Typically "{First Author} et al. {Year}"
  • BioProject: The BioProject unique identifier for the dataset.
  • Organism: The species of the organism from which the data was generated.
  • # Samples: The number of unique samples for this study
  • Date: Date of data deposition
  • ENA/SRA: Links to the study on the Sequence Read Archive and European Nucleotide Archive

Download Files

Users can download the following files from the RiboSeq Data Portal:

  • Reads: Collapsed Read Files in FASTA format. Unique reads from raw file with counts stored in FASTA header '>seq{read_number}_x{read_count}'
  • Alignment: The alignment of the reads to the reference genome in collapsed BAM format. Read name same as above
  • Profiles: The ribosome footprint positions in BigWig format (forward and reverse strand)
  • FastQC report: Report generated by FastQC
  • FastP report: Report generated by FastP

RDP Versions

Users can download the metadata from past versions: