Evidence map›Paper›PMID 34167459›Full record

ArticleBMC bioinformatics2021

VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments.

Yingbo Cui, Zihang Wang, Johannes Köster, Xiangke Liao, Shaoliang Peng, Tao Tang, Chun Huang, Canqun Yang

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Review
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Yingbo Cui *School of Computer, National University of Defense Technology, Changsha, 410073, China. yingbocui@nudt.edu.cn.ORCID http://orcid.org/0000-0003-4000-4957
Zihang Wang *College of Information Science and Engineering, Hunan University, Changsha, 410006, China.
Johannes KösterAlgorithms for Reproducible Bioinformatics, Institute of Human Genetics, University of Duisburg-Essen, 45147, Essen, Germany.
Xiangke LiaoSchool of Computer, National University of Defense Technology, Changsha, 410073, China.
Shaoliang PengCollege of Information Science and Engineering, Hunan University, Changsha, 410006, China.
Tao TangSchool of Computer, National University of Defense Technology, Changsha, 410073, China.
Chun HuangSchool of Computer, National University of Defense Technology, Changsha, 410073, China.
Canqun YangSchool of Computer, National University of Defense Technology, Changsha, 410073, China.

Funding

Key Technologies Research and Development Program 2020YFA0709800Key Technologies Research and Development Program (CN) 2018YFB0204301National Natural Science Foundation of China-Yunnan Joint Fund 61772543National Outstanding Youth Science Fund Project of National Natural Science Foundation of China 61972408
6 · The paper itself

Abstract

backgroundVISPR is an interactive visualization and analysis framework for CRISPR screening experiments. However, it only supports the output of MAGeCK, and requires installation and manual configuration. Furthermore, VISPR is designed to run on a single computer, and data sharing between collaborators is challenging.

resultsTo make the tool easily accessible to the community, we present VISPR-online, a web-based general application allowing users to visualize, explore, and share CRISPR screening data online with a few simple steps. VISPR-online provides an exploration of screening results and visualization of read count changes. Apart from MAGeCK, VISPR-online supports two more popular CRISPR screening analysis tools: BAGEL and JACKS. It provides an interactive environment for exploring gene essentiality, viewing guide RNA (gRNA) locations, and allowing users to resume and share screening results.

conclusionsVISPR-online allows users to visualize, explore and share CRISPR screening data online. It is freely available at http://vispr-online.weililab.org , while the source code is available at https://github.com/lemoncyb/VISPR-online .

Indexed as

Clustered Regularly Interspaced Short Palindromic RepeatsSoftwareInternetResearchRNA, Guide, CRISPR-Cas SystemsRNA, Guide, CRISPR-Cas SystemsCRISPRCRISPR screeningVISPRVisualization

Identifiers

PMID34167459
PMCPMC8223366

What OpenQuestion holds

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LicenceCC BY
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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.