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Science Research Weekly
By Mark R WilliamsonScience
Science Research Weekly episodes
- Episode 4: To Err in R is Human
Get ready for the top 10 errors in R, self-assembling peptides, microbiome mishaps, a theory-defying dwarf planet ring system, and a chance to save tiny hearts. Science On.
References
- The virtual microbiome: A computational framework to evaluate microbiome analyses
- A dense ring of the trans-Neptunian object Quaoar outside its Roche limit
- 3D Printing of Self-Assembling Nanofibrous Multidomain Peptide Hydrogels
- This one-atom chemical reaction could transform drug discovery
- logitr: Fast Estimation of Multinomial and Mixed Logit Models with Preference Space and Willingness-to-Pay Space Utility Parameterizations
- Python 3.11.2, Python 3.10.10 and 3.12.0 alpha 5 are available
- How to use Git to share SAS programs
- Top 10 errors in R and how to fix them
- NIH: Using Multimodal Biomarkers to Differentially Diagnose ADRDs for Clinical Trials
- NSF: Accelerating Research Translation
- Saving Tiny Hearts Society: Research Grants
R packages
- deFit: Fitting Differential Equations to Time Series Data
- synMicrodata: Synthetic Microdata Generator
- animate: A Web-Based Graphics Device for Animated Visualisations
- formatBibtex: Format BibTeX Entries and Files
6 min - Episode 3: The Ocean that Snuck up on Me
Get ready for heart-attack healing hydrogels, super rare supernovas, volumes of viroid sequences, stealth oceans, finding hex logos and packages by topic in CRAN, and NASA funding for exobiology. Science On.
References
- This groundbreaking biomaterial heals tissues from the inside out
- A high-mass X-ray binary descended from an ultra-stripped supernova
- Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs
- Tracking the Evolution of an Ocean Within Mimas Using the Herschel Impact Basin
- Journal of Statistical Software Volume 105
- Annual Julia Growth Statistics - January 2023
- Tips for organizing your R code
- December 2022: “Top 40” New CRAN Packages
- NASA: Exobiology- Living Systems Science
- NIH: Data Harmonization, Curation and Secondary Analysis of Existing Clinical Datasets
- DOD: Peer Reviewed Medical, Discovery Award
- DE-FOA: 2023 Exploratory Research for Extreme Scale Science
- NIH NOSI: Development of Functional Assay Sites to Evaluate Candidate -Omics Variants Associated with Heart, Lung, Blood, or Sleep Disease
- NIH NOSI: Revision Applications to add a Curation and Informatics Component to existing Animal and Biological Material Resource Centers
R-packages
- hexFinder: Find Hex Logos for CRAN Packages
- vvsculptor: Apply Manipulations to Data Frames
- findPackage: Find 'CRAN' Package by Topic
6 min - Episode 2: What Double Teeth You Have
Get ready for new deep sea bacterial phyla, extra ancient caecilian fossils, R Journal Volume 14/3 JuliaHub 6.0, visualizing star maps in R, and an IceCube neutrino competition! Science Research Weekly covers 3 topic areas: Research Articles, Research Tools, and Research Funding. Science On.
References
- Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits
- Chem-map profiles drug binding to chromatin in cells
- Study offers first glimpse of how many suffer from previously unknown illness
- Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin
- Triassic stem caecilian supports dissorophoid origin of living amphibians
- The R Journal Volume 14/3
- Star Map with R
- Show all data in the background of your faceted ggplot
- Fitting robust non-Gaussian models in Stan and R-INLA
- JuliaHub 6.0 Features Released
- Kaggle Competition: IceCube - Neutrinos in Deep Ice
- NSF: Molecular Foundations for Biotechnology
- NSF: Expanding Capacity in Quantum Information Science and Engineering
- DE: Scientific Machine Learning for Complex Systems
- AFOSR: Fiscal Year 2023 Science, Technology, Engineering and Mathematics (STEM) Program
R-packages
- neatR: Neat Data for Presentation
- polyglotr: Translate Text
- clarify: Simulation-Based Inference for Regression Models
- poolHelper: Simulates Pooled Sequencing Genetic Data
- vDiveR: Visualization of Viral Protein Sequence Diversity Dynamics
8 min - Episode 1: An Explosive Beginning
Welcome to Science Research Weekly, the successor to my first podcast, Statistics Weekly. This abbreviated trial run of an episode includes: a research article on microbes from a volcanic island, the largest stellar catalogue to date, Arduino project ideas for 2023, and NSF Research and Development grants.
References:
- The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga
- A high-quality Ixodes scapularis genome advances tick science
- Haplotype-aware pantranscriptome analyses using spliced pangenome graphs
- The molecular evolution of genes previously associated with large sizes reveals possible pathways to cetacean gigantism
- The Dark Energy Camera Plane Survey 2 (DECaPS2): More Sky, Less Bias, and Better Uncertainties
- Volume 105 of the Journal of Statistical Software
- 12 blog posts from 2022 that deserve a second look
- Top 15 Stunning Arduino Project Ideas For 2023
- Some R Conferences for 2023
- Web scraping in R
- Imputation in R: Top 3 Ways for Imputing Missing Data
- FDA: Fellowship in Understanding Pathogenesis and Improving Detection of Flaviviruses
- NSF: Future Manufacturing
- NSF: Division of Environmental Biology
- NSF: Division of Molecular and Cellular Biosciences Core Programs
- NSF: Division of Integrative Organismal Systems Core Programs
- NIH NOSI: Research on the Etiology, Early Detection, Screening and Prevention of Early-Onset Colorectal Cancer
- NIH NOSI: Computational and Statistical Methods to Enhance Discovery from Health Data
R packages:
- ggplate: Create Layout Plots of Biological Culture Plates and Microplates
- glmmrOptim: Approximate Optimal Experimental Designs Using Generalised Linear Mixed Models
- shiny.benchmark: Benchmark the Performance of 'shiny' Applications
- blindreview: Blind Review Using Forward Search Procedures
- metabias: Meta-Analysis for Within-Study and/or Across-Study Biases
- evoTS: Analyses of Evolutionary Time-Series
- OssaNMA: Optimal Sample Size and Allocation with a Network Meta-Analysis
8 min - Science Research Weekly Trailer
Welcome to Science Research Weekly. This is the successor to my first podcast, Statistics Weekly. Every week, I will cover 3 topic areas: Research Articles, Research Tools, and Research Funding. Check out the accompanying blog at: https://scienceresearchweekly.wordpress.com/
1 min - 1 min
- Episode 39: Last Stat Before Christmas
In this episode, I pondered the problem of false positives in publications, rotated around the JuliaHub, machinated over machine learning projects, and put R package ‘drawCell’ to the test.
References:
- Are most published research findings false in a continuous universe?
- Principal component analysis
- A no-free-lunch theorem for multitask learning
- JuliaHub
- Signal-to-noise ratio and statistical tests
- Large Enough Sample Condition
- Top 11 Interesting Machine Learning Project Ideas For 2023
- Code longevity of the R programming language
- {drawCell} – R package and Shiny app for drawing cell structures
R-packages:
- colorRamp2: Generate Color Mapping Functions
- rworkflows: Test, Document, Containerise, and Deploy R Packages
- MetChem: Chemical Structural Similarity Analysis
- panelsummary: Create Publication-Ready Regression Tables with Panels
- arf: Adversarial Random Forests
5 min - Episode 38: Ho, Ho, Holiday Statistics Projects
In this episode, I marched through machine learning abstractions, brought home the BQN, discovered statistics projects to work on over Christmas, and found the Gosling that lays the golden egg,
References:
- Quantifying uncertainty of machine learning methods for loss given default
- Evaluating the performance of memory type logarithmic estimators using simple random sampling
- A fast kernel independence test for cluster-correlated data
- Autoencoders for sample size estimation for fully connected neural network classifiers
- [R-pkgs] onetime 0.1.0: Run Code Only Once
- 🚧 WIP 🚧 From Julia to BQN
- Using SAS to score a test
- Using the cspade action to find frequent gene sequences
- The easygoing relationship between computer scientists and null hypothesis significance testing
- Top 11+ Coding Projects for Beginners (2023 Edition)
- Gosling: Interactive Genomics Charts in R Shiny
- Gosling Main Page
R-packages:
- POMS: Phylogenetic Organization of Metagenomic Signals
- macroBiome: A Tool for Mapping the Distribution of the Biomes and Bioclimate
- reservr: Fit Distributions and Neural Networks to Censored and Truncated Data
- NPCox: Nonparametric and Semiparametric Proportional Hazards Model
7 min - Episode 37: Hexadecimal Codes of Christmas
In this episode, I got into the spirit of Sinterklaas with Python, jumpstarted Julia learning, cleared up confusion between ANOVA and regression results, and color paletted the night away.
References:
- Estimation of population variance under ranked set sampling method by using the ratio of supplementary information with study variable
- 10 Simple Reasons to Learn the Julia Programming Language (in 2023)
- Python 3.11.1, 3.10.9, 3.9.16, 3.8.16, 3.7.16, and 3.12.0 alpha 3 are now available
- Art in SAS: Christmas wrapping paper
- when the results of your anova table and regression coefficients disagree
- Select colours from an image in R with {eyedroppeR}
- How to make your own #RStats Wrapped!
R-packages:
- HodgesTools: Common Use Tools for Genomic Analysis
- DependencyReviewer: Tool Suite to Investigate Other Packages
- gmvjoint: Joint Models of Survival and Multivariate Longitudinal Data
- r2social: App Inclusion of Social Sharing and Connect Buttons
- lterpalettefinder: Extract Color Palettes from Photos and Pick Official LTER Palettes
- jackknifeR: Jackknife Linear Regression and Correlation
- POMADE: Power for Meta-Analysis of Dependent Effects
- HTT: Hypothesis Testing Tree
6 min - Episode 36: Curb your Stats-thusiasm
In this episode, I picked the choicest R journal articles, served up a digital poker hand in SAS, and tried not to let a defective R-package get me down.
References:
- brolgar: An R package to BRowse Over Longitudinal Data Graphically and Analytically in R
- shinybrms: Fitting Bayesian Regression Models Using a Graphical User Interface for the R Package brms
- R-miss-tastic: a unified platform for missing values methods and workflows
- Bias reduction in the logistic model parameters with the LogF(1,1) penalty under MAR assumption
- A simulation study: Using dual ancillary variable to estimate population mean under stratified random sampling
- Multi-omics peripheral and core regions of cancer
- Efficient and automated bandwidth selection in SAS PROC KPCA
- Simulate poker hands in SAS
- Covariates: Definition & Uses
- Our First Peer-Reviewed Statistical R Packages!
- Navigating folders in RStudio: a beginner’s guide
- October 2022: “Top 40” New CRAN Packages
R-packages:
- HTT: Hypothesis Testing Tree
- boxfilter: Filter Noisy Data
- ggpcp: Parallel Coordinate Plots in the 'ggplot2' Framework
- StatTeacherAssistant: An App that Assists Intro Statistics Instructors with Data Sets
- tidyclust: A Common API to Clustering
6 min
About Science Research Weekly
From the publisher's feed
A weekly overview of helpful scientific research topics and the successor of the podcast Statistics Weekly. Every week, I will cover 3 topic areas: Research Articles, Research Tools, and Research…
Funding. Science On.