ArticleBiology methods & protocols2020
ShinyButchR: Interactive NMF-based decomposition workflow of genome-scale datasets.
Article in Biology methods & protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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.
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.
Who cites it
9 citing papers in PubMed, 17 citations in OpenAlex.
- Immunogenic Cell Death-relevant Molecular Patterns, Prognostic Genes, and Implications for Immunotherapy in Ovarian Cancer.Current medicinal chemistry · 2026Article
- A new IDH-independent hypermethylation phenotype is associated with astrocyte-like cell state in glioblastoma.Genome biology · 2025Article
- CRISPR-Cas9 screening identified novel subtypes of cutaneous melanoma based on essential cancer genes.Archives of dermatological research · 2024Article
- A clustering approach to improve our understanding of the genetic and phenotypic complexity of chronic kidney disease.Scientific reports · 2024Article
- A clustering approach to improve our understanding of the genetic and phenotypic complexity of chronic kidney disease.medRxiv : the preprint server for health sciences · 2023Article
- Improving Diagnostics with Deep Forest Applied to Electronic Health Records.Sensors (Basel, Switzerland) · 2023Article
- dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning.Bioinformatics (Oxford, England) · 2022Article
- Identification of Novel Subtypes in Lung Adenocarcinoma: Evidence from Gene Set Variation Analysis in Tumor and Adjacent Nontumor Samples.Disease markers · 2022Article
- Identification of Specific Cervical Cancer Subtypes and Prognostic Gene Sets in Tumor and Nontumor Tissues Based on GSVA Analysis.Journal of oncology · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Non-negative matrix factorization (NMF) has been widely used for the analysis of genomic data to perform feature extraction and signature identification due to the interpretability of the decomposed signatures. However, running a basic NMF analysis requires the installation of multiple tools and dependencies, along with a steep learning curve and computing time. To mitigate such obstacles, we developed ShinyButchR, a novel R/Shiny application that provides a complete NMF-based analysis workflow, allowing the user to perform matrix decomposition using NMF, feature extraction, interactive visualization, relevant signature identification, and association to biological and clinical variables. ShinyButchR builds upon the also novel R package ButchR, which provides new TensorFlow solvers for algorithms of the NMF family, functions for downstream analysis, a rational method to determine the optimal factorization rank and a novel feature selection strategy.
Identifiers
What OpenQuestion holds
Registered trials
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.