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@unknown

Apr 18 • 7 tweets • 4 min read Twitter logo

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1/ Bioinformatics is an essential part of modern biology, and R is a powerful programming language that has become the standard tool for bioinformatics analysis. #rstats #bioinformatics #datascience

2/ R provides an extensive collection of packages for bioinformatics analysis, including tools for gene expression analysis, sequencing data analysis, and network analysis. #rstats #bioinformatics

3/ Bioconductor is an open-source software project that provides tools for the analysis and comprehension of genomic data. It contains more than 1,800 packages for bioinformatics analysis. #rstats #bioinformatics

4/ DESeq2, edgeR, and limma are popular packages for differential gene expression analysis. These packages allow researchers to identify genes that are differentially expressed between two or more groups of samples. #rstats #bioinformatics

5/ clusterProfiler is a package for gene set enrichment analysis. It allows researchers to identify biological pathways that are over-represented in a set of differentially expressed genes. #rstats #bioinformatics

6/ R is also a great tool for analyzing sequencing data, such as RNA-seq, ChIP-seq, and ATAC-seq. Some popular R packages for sequencing data analysis include Rsubread, QuasR, and ShortRead. #rstats #bioinformatics

7/ R provides an extensive collection of bioinformatics packages that allow researchers to perform a wide range of analyses on genomic and sequencing data. These tools are essential for understanding the complex biological processes that underlie disease and development. #rstats

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Apr 19

1/10: 🧵 Welcome to this thread on #regression modeling strategies in #R! We'll discuss key techniques and packages to help you build effective models. Ready to dive in? Let's go! 🚀 #RStats #DataScience #Statistics

2/10: 🌐 Linear Regression: Start with simple & multiple linear regression using 'lm()' function. Check out the 'broom' package for easy-to-use regression output! #RStats cran.r-project.org/web/packages/b…

3/10:🏞️ Polynomial Regression: When data is nonlinear, try polynomial regression! Use 'poly()' to create higher-order terms. Beware of overfitting! #RStats

Read 10 tweets

Twitter author

Apr 18

1/ Regularization methods are a crucial part of machine learning models that help to prevent overfitting. In R, there are several popular regularization methods available, including Lasso, Ridge, and Elastic Net. #rstats #datascience #MachineLearning

2/ Lasso (Least Absolute Shrinkage and Selection Operator) is a method that uses L1 regularization to shrink the coefficients of less important features to zero, resulting in a sparse model. It is useful when there are many features with only a few of them being relevant. #rstats

3/ Ridge regression, on the other hand, uses L2 regularization to add a penalty term to the loss function that shrinks the coefficients of less important features towards zero without setting them to zero. It is useful when all features are potentially relevant. #rstats

Read 9 tweets

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Apr 18

1/6: Venn diagrams are commonly used in bioinformatics to visualize the overlap of different sets of genes or proteins. There are several R packages available for creating these diagrams, including VennDiagram, ggvenn, and ggVennDiagram. #rstats #datascience #bioinformatics

2/6: VennDiagram is a widely used package for creating classic Venn diagrams with up to six sets. It offers a range of options for customizing the appearance of the diagram, including font size, color, and label placement. #rstats #bioinformatics

3/6: One of the advantages of VennDiagram is the ability to easily incorporate statistical analyses. For example, you can calculate the significance of the overlap between different sets of genes or proteins and display this information on the diagram. #rstats #bioinformatics

Read 6 tweets

Twitter author

Apr 18

1/ Mixed models are a powerful statistical tool for analyzing complex data with both fixed and random effects. R has several great packages for fitting mixed models. #rstats #datascience

2/ One of the most popular packages for mixed models in R is "lme4". This package provides functions for fitting linear and generalized linear mixed models, including models with crossed and nested random effects. #rstats #lme4 cran.r-project.org/web/packages/l…

3/ Another popular mixed model package in R is "nlme". It has similar functionality to "lme4" but is designed to handle longitudinal or repeated-measures data. #rstats #nlme cran.r-project.org/web/packages/n…

Read 6 tweets

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Apr 17

1/ If you're designing experiments, check out the "randomizeR" package in R! It helps you create randomized experimental designs, which can be crucial for avoiding bias and ensuring your results are statistically sound. #rstats #datascience cran.r-project.org/web/packages/r…

2/ Another helpful package is "DoE.base", which offers a wide range of tools for design and analysis of experiments. You can use it to create custom designs, analyze data, and more. #rstats #datascience cran.r-project.org/web/packages/D…

3/ "FrF2" is another package you'll want to consider for experiment design. It helps you create fractional factorial designs, which can save time and resources while still giving you the information you need. #rstats #datascience cran.r-project.org/web/packages/F…

Read 5 tweets

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Apr 17

1/ In 2021, DeepMind made headlines when it announced that it had developed an algorithm called AlphaFold that could predict the 3D structure of proteins with remarkable accuracy. Here's what you need to know about this groundbreaking technology. #bioinformatics #AlphaFold #AI

2/ Proteins are essential building blocks of life, and their structure is critical to understanding how they function. Determining the structure of a protein can be a long and complex process, but AlphaFold is changing that.

3/ AlphaFold uses deep neural networks to predict the 3D structure of a protein based on its amino acid sequence. By training on a vast database of known protein structures, AlphaFold can accurately predict the structure of a protein in a matter of days, rather than years.

Read 7 tweets

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