ArticleBioinformatics (Oxford, England)2017
OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed.
- Graph 'texture' features as novel metrics that can summarize complex biological graphs.Physics in medicine and biology · 2023Article
- EvAM-Tools: tools for evolutionary accumulation and cancer progression models.Bioinformatics (Oxford, England) · 2022Article
- Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?PLoS computational biology · 2021Article
- CellCoal: Coalescent Simulation of Single-Cell Sequencing Samples.Molecular biology and evolution · 2020Article
- Every which way? On predicting tumor evolution using cancer progression models.PLoS computational biology · 2019Article
- Estimating the predictability of cancer evolution.Bioinformatics (Oxford, England) · 2019Article
- Cancer progression models and fitness landscapes: a many-to-many relationship.Bioinformatics (Oxford, England) · 2018Article
- SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution.Bioinformatics (Oxford, England) · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryOncoSimulR implements forward-time genetic simulations of biallelic loci in asexual populations with special focus on cancer progression. Fitness can be defined as an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, restrictions in the order of accumulation of mutations, and order effects. Mutation rates can differ among genes, and can be affected by (anti)mutator genes. Also available are sampling from simulations (including single-cell sampling), plotting the genealogical relationships of clones and generating and plotting fitness landscapes. AVAILABILITY AND IMPLEMENTATION: Implemented in R and C ++, freely available from BioConductor for Linux, Mac and Windows under the GNU GPL license. Version 2.5.9 or higher available from: http://www.bioconductor.org/packages/devel/bioc/html/OncoSimulR.html . GitHub repository at: https://github.com/rdiaz02/OncoSimul. CONTACT: ramon.diaz@iib.uam.es. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
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.