Biostatsquid
Biostatsquid
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Detect and remove doublets in R (scRNAseq)
In this tutorial I will explain how to remove doublets from scRNAseq data in R using R package after running one or more doublet detection tools. For this tutorial, I’ll be using RStudio, and you’ll need the tidyverse packages as well as Seurat.
You will learn how to:
- get doublet/singlet count and percentage for one or more doublet detection tools
-get doublet vs singlets stats
-remove high-confidence doublets from your Seurat object
- and more!
And as always, you can find the code I am using in this tutorial at biostatsquid.com, where you can also find a step by step explanation of the code. For this tutorial you will need R, or Rstudio, and you will need to install the package listed above.
Hope you like it!
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• simple and clear explanations of biostatistics methods
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Переглядів: 138

Відео

Easy DoubletFinder tutorial in R (scRNAseq)
Переглядів 214Місяць тому
In this tutorial I will explain how to detect and remove doublets from scRNAseq data in R using R package DoubletFinder. For this tutorial, I’ll be using RStudio, and you’ll need the package DoubletFinder. You will learn how to: - run DoubletFinder -get doublet vs singlets stats -add doublet/singlet annotations to your Seurat object - and more! And as always, you can find the code I am using in...
Easy doublet detection in R with scDoubletFinder (scRNAseq)
Переглядів 216Місяць тому
In this tutorial I will explain how to detect and remove doublets from scRNAseq data in R using R package scDoubletFinder(). For this tutorial, I’ll be using RStudio, and you’ll need the package scDoubletFinder. You will learn how to: - run scDoubletFinder -get doublet vs singlets stats -add doublet/singlet annotations to your Seurat object - and more! And as always, you can find the code I am ...
How does doublet finder work? Easy explanation!
Переглядів 2652 місяці тому
In this video, we will discuss the main concepts behind DoubletFinder, a doublet-finding tool for scRNAseq in R - easily explained! We will go through the main steps it uses to mark cells in your Seurat dataset as doublets. R tutorial coming up next! And as always, you can find the full explanation at biostatsquid.com: biostatsquid.com/ Hope you like it!
Violin plots tutorial with ggplot2 in R (part 2)
Переглядів 2023 місяці тому
In this tutorial I will explain how to create and customise your own violin plots in R. In particular, we will cover facet_wrap, facet_grid, and how to create your own violin plot function. For this tutorial, I’ll be using RStudio, and you’ll need the package ggplot2. You will learn how to: - plot a violin plot in R - customise and edit labels, colours, themes - plot grouped violin plots - and ...
Violin plots tutorial with ggplot2 in R (part 1)
Переглядів 6373 місяці тому
In this tutorial I will explain how to create and customise your own violin plots in R. For this tutorial, I’ll be using RStudio, and you’ll need the package ggplot2. You will learn how to: - plot a violin plot in R - customise and edit labels, colours, themes - plot grouped violin plots - and more! And as always, you can find the code I am using in this tutorial at biostatsquid.com, where you ...
EASY violin plots and boxplots - simple explanation with examples
Переглядів 4994 місяці тому
In this video, we will discuss the main concepts behind violin plots and boxplots - easily explained! We will go through what are violin plots and boxplots and how to interpret it and use it to visualise our biological data. And as always, you can find the full explanation at biostatsquid.com: biostatsquid.com/interpret-density-plots/ Hope you like it! Watched it already? If you liked this vide...
How to interpret density plots - simple explanation with examples!
Переглядів 1,8 тис.5 місяців тому
In this video, we will discuss the main concepts behind density plots - easily explained! We will go through what is a density plot and how to interpret it and use it to visualise our biological data. And as always, you can find the full explanation at biostatsquid.com: biostatsquid.com/interpret-density-plots/ Hope you like it! Watched it already? If you liked this video or found it useful, pl...
Logistic regression - easily explained with an example!
Переглядів 1,3 тис.6 місяців тому
In this video, we will discuss the main concepts behind Logistic regression - easily explained! We will go through what is logistic regression, when to use it and how to interpret the coefficients. And as always, you can find the full explanation at biostatsquid.com Hope you like it! biostatsquid.com/easy-logistic-regression/ Watched it already? If you liked this video or found it useful, pleas...
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Переглядів 1,5 тис.7 місяців тому
In this tutorial I will explain how to do cell type annotation with the R package SingleR. After a brief introduction to reference-based automatic cell type annotation and SingleR, we will go step by step through the workflow, including preparing our input data, running SingleR, interpreting the results and some tips and tricks to get the most out of SingleR. For this tutorial, I’ll be using RS...
COMPLETE SURVIVAL ANALYSIS tutorial in R: Kaplan-Meier, Cox regression, Forest Plots...
Переглядів 7 тис.9 місяців тому
In this tutorial, I will explain how to perform survival analysis in R, including log rank test, Cox regression, Kaplan-Meier curves, and more! We will use the R packages ggsurvplot, survminer and survival. You will learn how to: - plot a Kaplan Meier curve - test for differences between groups using the log rank test - build a survival model with Cox regression - and visualise your results wit...
COX REGRESSION and HAZARD RATIOS - easily explained with an example!
Переглядів 19 тис.10 місяців тому
In this video, we will discuss the main concepts behind Cox regression for survival time analysis - easily explained! We will go through hazard ratios, coefficients, p-values and confidence intervals. I will also give you simple and practical guidelines on how to interpret the results from Cox regression, with an example! And as always, you can find the full explanation at biostatsquid.com Hope...
LOG RANK TEST for survival analysis - easily explained with an example!
Переглядів 7 тис.11 місяців тому
In this video, we will discuss the main concepts behind the Log Rank Test - easily explained! I will also give you simple and practical guidelines on how to interpret the results from the Log Rank test And as always, you can find the full explanation at biostatsquid.com Hope you like it! biostatsquid.com/easy-log-rank-test/ Watched it already? If you liked this video or found it useful, please ...
How to interpret KAPLAN-MEIER curves - Easily explained!
Переглядів 15 тис.11 місяців тому
In this video, we will discuss the main concepts behind Kaplan-Meier curves- easily explained! I will also give you simple and practical guidelines on how to interpret a Kaplan-Meier curve. And as always, you can find the full explanation at biostatsquid.com Hope you like it! biostatsquid.com/kaplan-meier-curve/ Watched it already? If you liked this video or found it useful, please let me know!...
Easy survival analysis - simple introduction with an example!
Переглядів 2,7 тис.11 місяців тому
In this video, we will discuss the main concepts behind survival time analysis - easily explained! Survival time analysis is really common in biostatistics. You might have heard of Kaplan-Meier curves, Cox regressions or the log rank test. In clinical trials, survival time analysis is used to compare the performance of two different kinds of treatment, for example. Survival time analysis can al...
Top tips to create pretty plots in R (ggplot2)
Переглядів 1,3 тис.Рік тому
Top tips to create pretty plots in R (ggplot2)
Gene Set Enrichment Analysis (GSEA) with fgsea - easy R tutorial
Переглядів 10 тис.Рік тому
Gene Set Enrichment Analysis (GSEA) with fgsea - easy R tutorial
Pathway Enrichment Analysis plots: easy R tutorial
Переглядів 9 тис.Рік тому
Pathway Enrichment Analysis plots: easy R tutorial
Pathway enrichment analysis tutorial in R with clusterProfiler()
Переглядів 15 тис.Рік тому
Pathway enrichment analysis tutorial in R with clusterProfiler()
Step-by-step heatmap tutorial in R with pheatmap()
Переглядів 11 тис.Рік тому
Step-by-step heatmap tutorial in R with pheatmap()
How to interpret a heatmap for differential gene expression analysis - simply explained!
Переглядів 20 тис.Рік тому
How to interpret a heatmap for differential gene expression analysis - simply explained!
Mapping and aligning sequencing reads | NGS read preprocessing in R (Part 3)
Переглядів 611Рік тому
Mapping and aligning sequencing reads | NGS read preprocessing in R (Part 3)
Quality check on sequencing reads | NGS read preprocessing in R (Part 2)
Переглядів 798Рік тому
Quality check on sequencing reads | NGS read preprocessing in R (Part 2)
Quality check on sequencing reads | NGS read preprocessing in R (Part 1)
Переглядів 3,4 тис.Рік тому
Quality check on sequencing reads | NGS read preprocessing in R (Part 1)
Standard scRNAseq preprocessing workflow with Seurat | Beginner R
Переглядів 7 тис.Рік тому
Standard scRNAseq preprocessing workflow with Seurat | Beginner R
How to interpret GSEA results and plot - simple explanation of ES, NES, leading edge and more!
Переглядів 27 тис.Рік тому
How to interpret GSEA results and plot - simple explanation of ES, NES, leading edge and more!
Gene Set Enrichment Analysis (GSEA) - simply explained!
Переглядів 31 тис.Рік тому
Gene Set Enrichment Analysis (GSEA) - simply explained!
Pathway enrichment analysis - simple explanation!
Переглядів 25 тис.Рік тому
Pathway enrichment analysis - simple explanation!
FDR, q-values vs p-values: multiple testing simply explained!
Переглядів 11 тис.Рік тому
FDR, q-values vs p-values: multiple testing simply explained!
Correlation vs causation | Simple explanation with examples
Переглядів 3,3 тис.Рік тому
Correlation vs causation | Simple explanation with examples

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