Evidence map›Paper›PMID 38260303›Full record

ArticlebioRxiv : the preprint server for biology2024

RiboGraph: An interactive visualization system for ribosome profiling data at read length resolution.

Jonathan Chacko, Hakan Ozadam, Can Cenik

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

3 authors.

Jonathan ChackoDepartment of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
Hakan OzadamDepartment of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
Can CenikDepartment of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.ORCID 0000-0001-6370-0889

Funding

Single cell quantification of translation control in early mouse developmentR35GM150667 · NIGMS · UNIVERSITY OF TEXAS AT AUSTIN · PI Can Cenik · 2023 to 2026
$1.6M
Translational regulation of limb bud initiationR21HD110096 · NICHD · UNIVERSITY OF TEXAS AT AUSTIN · PI CENIK, CAN, VOKES, STEVEN ALEXANDER · 2022 to 2023
$436k
NICHD NIH HHS R21 HD110096NIGMS NIH HHS R35 GM150667
6 · The paper itself

Abstract

Ribosome profiling is a widely-used technique for measuring ribosome occupancy at nucleotide resolution. However, the need to analyze this data at nucleotide resolution introduces unique challenges in data visualization and analyses. In this study, we introduce RiboGraph, a dedicated visualization tool designed to work with .ribo files, a specialized and efficient format for ribosome occupancy data. Unlike existing solutions that rely on large alignment files and time-consuming preprocessing steps, RiboGraph operates on a purpose designed compact file type and eliminates the need for data preprocessing. This efficiency allows for interactive, real-time visualization at ribosome-protected fragment length resolution. By providing an integrated toolset, RiboGraph empowers researchers to conduct comprehensive visual analysis of ribosome occupancy data. Availability and Implementation: Source code, step-by-step installation instructions and links to documentation are available on GitHub: https://github.com/ribosomeprofiling/ribograph. On the same page, we provide test files and a step-by-step tutorial highlighting the key features of RiboGraph.

Indexed as

InteractiveRiboRibo-SeqRibosome profilingSoftwareTranslationVisualization

Identifiers

PMID38260303
PMCPMC10802566

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.