Evidence map›Paper›PMID 39365707›Full record

ArticleBioinformatics (Oxford, England)2024

PCBS: an R package for fast and accurate analysis of bisulfite sequencing data.

Kathryn Lande, April E Williams

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

2 authors.

Kathryn LandeThe Razavi Newman Integrative Genomics and Bioinformatics Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States.ORCID 0009-0005-1613-8981
April E WilliamsThe Razavi Newman Integrative Genomics and Bioinformatics Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States.

Funding

Project 4: Interrogating and harnessing age-related IFN signaling and innate immunity in HCC prevention and therapyP01AG073084 · NIA · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI PETER D. ADAMS, GERALD SHADEL · 2021 to 2026
$13.6M
San Diego Nathan Shock CenterP30AG068635 · NIA · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI SHADEL, GERALD · 2020 to 2024
$6.0M
NIA NIH HHS AG073084NIA NIH HHS P01 AG073084NIA NIH HHS P30 AG068635NIH
6 · The paper itself

Abstract

motivationWhole-genome bisulfite sequencing is a powerful tool for analyzing chromatin methylation genome-wide, but analysis of whole-genome bisulfite data is slow, inflexible, and often inaccurate.

resultsWe developed PCBS (Principal Component BiSulfite), a computationally efficient R package for Whole Genome Bisulfite Sequencing analysis that demonstrates remarkable accuracy and flexibility compared to current tools. PCBS identifies differentially methylated loci, differentially methylated regions, and offers novel functionality that allows for more targeted methylation analyses. PCBS uses minimal computational resources; a complete pipeline in mouse can run on a local RStudio instance in a matter of minutes. AVAILABILITY AND IMPLEMENTATION: PCBS is an R package available under a GNU GPLv3 license on GitHub: https://github.com/katlande/PCBS and CRAN: https://CRAN.R-project.org/package=PCBS. Instructions for use are available at: https://katlande.github.io/PCBS/.

Indexed as

DNA MethylationSoftwareAnimalsMiceSequence Analysis, DNASulfitesWhole Genome Sequencinghydrogen sulfiteSulfites

Identifiers

PMID39365707
PMCPMC11471259

What Socratic holds

Textmetadata
LicenceCC BY
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 Socratic graph.