How to create pseudobulk from single-cell RNAseq data

What is pseduobulk? Many of you have heard about bulk-RNAseq data. What is pseduobulk? Single-cell RNAseq can profile the gene expression at single-cell resolution. For differential expression, psedobulk seems to perform really well(see paper muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data). To create a pseudobulk, one can artificially add up the counts for cells from the same cell type of the same sample. In this blog post, I’ll guide you through the art of creating pseudobulk data from scRNA-seq experiments.

multi-omics data integration: a case study with transcriptomics and genomics mutation data

Multi-omics data analysis is a cutting-edge approach in biology that involves studying and integrating information from multiple biological “omics” sources. These omics sources include genomics (genes and their variations), transcriptomics (gene expression and RNA data), proteomics (proteins and their interactions), metabolomics (small molecules and metabolites), epigenomics (epigenetic modifications), and more. By analyzing data from various omics levels together, we can gain a more comprehensive and detailed understanding of biological systems and their complexities.

How to do neighborhood/cellular niches analysis with spatial transcriptome data

Sign up for my newsletter to not miss a post like this https://divingintogeneticsandgenomics.ck.page/newsletter In a previous blog post, I showed you how to make a Seurat spatial object from Vizgen spatial transcriptome data. In this post, I am going to show you how to identify clusters of neighborhood or cellular niches where specific cell types tend to co-localize. read in the data and pre-process library(Seurat) library(here) library(ggplot2) library(dplyr) # the LoadVizgen function requires the raw segmentation files which is too big.

How to construct a spatial object in Seurat

Sign up for my newsletter to not miss a post like this https://divingintogeneticsandgenomics.ck.page/newsletter Single-cell spatial transcriptome data is a new and advanced technology that combines the study of individual cells’ genes and their location in a tissue to understand the complex cellular and molecular differences within it. This allows scientists to investigate how genes are expressed and how cells interact with each other with much greater detail than before.

How to make a triangle correlation heatmap with p-values labeled

In this blog post, I am going to show you how to make a correlation heatmap with p-values and significant values labeled in the heatmap body. Let’s use the PBMC single cell data as an example. You may want to read my previous blog post How to do gene correlation for single-cell RNAseq data. Load libraries library(dplyr) library(Seurat) library(patchwork) library(ggplot2) library(ComplexHeatmap) library(SeuratData) library(hdWGCNA) library(WGCNA) set.seed(1234) prepare the data data("pbmc3k") pbmc3k #> An object of class Seurat #> 13714 features across 2700 samples within 1 assay #> Active assay: RNA (13714 features, 0 variable features) ## routine processing pbmc3k<- pbmc3k %>% NormalizeData(normalization.

How to do gene correlation for single-cell RNAseq data (part 2) using meta-cell

In my last blog post, I showed that pearson gene correlation for single-cell data has flaws because of the sparsity of the count matrix. One way to get around it is to use the so called meta-cell. One can use KNN to find the K nearest neighbors and collapse them into a meta-cell. You can implement it from scratch, but one should not re-invent the wheel. For example, you can use metacells.

use random forest and boost trees to find marker genes in scRNAseq data

This is a blog post for a series of posts on marker gene identification using machine learning methods. Read the previous posts: logistic regression and partial least square regression. This blog post will explore the tree based method: random forest and boost trees (gradient boost tree/XGboost). I highly recommend going through https://app.learney.me/maps/StatQuest for related sections by Josh Starmer. Note, all the tree based methods can be used to do both classification and regression.

My odyssey of obtaining scRNAseq metadata

I want to curate a public scRNAseq dataset from this paper Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer ffq I first tried ffq, but it gave me errors. ffq fetches metadata information from the following databases: GEO: Gene Expression Omnibus, SRA: Sequence Read Archive, EMBL-EBI: European Molecular BIology Laboratory’s European BIoinformatics Institute, DDBJ: DNA Data Bank of Japan, NIH Biosample: Biological source materials used in experimental assays, ENCODE: The Encyclopedia of DNA Elements.

Obtain metadata for public datasets in GEO

There are so many public datasets there waiting for us to mine! It is the blessing and cursing as a computational biologist! Metadata, or the data describing (e.g., responder or non-responder for the treatment) the data are critical in interpreting the analysis. Without metadata, your data are useless. People usually go to GEO or ENA to download public data. I asked this question on twitter, and I will show you how to get the metadata as suggested by all the awesome tweeps.

Be careful when left_join tables with duplicated rows

This is going to be a really short blog post. I recently found that if I join two tables with one of the tables having duplicated rows, the final joined table also contains the duplicated rows. It could be the expected behavior for others but I want to make a note here for myself. library(tidyverse) df1<- tibble(key = c("A", "B", "C", "D", "E"), value = 1:5) df1 ## # A tibble: 5 x 2 ## key value ## <chr> <int> ## 1 A 1 ## 2 B 2 ## 3 C 3 ## 4 D 4 ## 5 E 5 dataframe 2 has two identical rows for B.