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.

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.

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.

How to test if two distributions are different

I asked this question on Twitter: what test to test if two distributions are different? I am aware of KS test. When n is large (which is common in genomic studies), the p-value is always significant. better to test against an effect size? how to do it in this context? In genomics studies, it is very common to have large N (e.g., the number of introns, promoters in the genome, number of cells in the single-cell studies).

dplyr::count misses factor levels: a case in comparing scRNAseq cell type abundance

It is very common to see in the scRNAseq papers that the authors compare cell type abundance across groups (e.g., treatment vs control, responder vs non-responder). Let’s create some dummy data. library(tidyverse) set.seed(23) # we have 6 treatment samples and 6 control samples, 3 clusters A,B,C # but in the treatment samples, cluster C is absent (0 cells) in sample7 sample_id<- c(paste0("sample", 1:6, "_control", rep(c("_A","_B","_C"),each = 6)), paste0("sample", 8:12, "_treatment", rep(c("_A","_B", "_C"), each = 5))) sample_id<- c(sample_id, "sample7_treatment_A", "sample7_treatment_B") cell_id<- paste0("cell", 1:20000) cell_df<- tibble::tibble(sample_id = sample(sample_id, size = length(cell_id), replace = TRUE), cell_id = cell_id) %>% tidyr::separate(sample_id, into = c("sample_id", "group", "clusterid"), sep= "") cell_num<- cell_df %>% group_by(group, cluster_id, sample_id)%>% summarize(n=n()) cell_num ## # A tibble: 35 x 4 ## # Groups: group, cluster_id [6] ## group cluster_id sample_id n ## <chr> <chr> <chr> <int> ## 1 control A sample1 551 ## 2 control A sample2 546 ## 3 control A sample3 544 ## 4 control A sample4 585 ## 5 control A sample5 588 ## 6 control A sample6 542 ## 7 control B sample1 550 ## 8 control B sample2 562 ## 9 control B sample3 574 ## 10 control B sample4 563 ## # … with 25 more rows total_cells<- cell_df %>% group_by(sample_id) %>% summarise(total = n()) total_cells ## # A tibble: 12 x 2 ## sample_id total ## <chr> <int> ## 1 sample1 1673 ## 2 sample10 1713 ## 3 sample11 1691 ## 4 sample12 1696 ## 5 sample2 1633 ## 6 sample3 1700 ## 7 sample4 1711 ## 8 sample5 1768 ## 9 sample6 1727 ## 10 sample7 1225 ## 11 sample8 1720 ## 12 sample9 1743 join the two dataframe to get percentage of cells per cluster per sample

customize FeaturePlot in Seurat for multi-condition comparisons using patchwork

Seurat is great for scRNAseq analysis and it provides many easy-to-use ggplot2 wrappers for visualization. However, this brings the cost of flexibility. For example, In FeaturePlot, one can specify multiple genes and also split.by to further split to multiple the conditions in the meta.data. If split.by is not NULL, the ncol is ignored so you can not arrange the grid. This is best to understand with an example. library(dplyr) library(Seurat) library(patchwork) library(ggplot2) # Load the PBMC dataset pbmc.

Monty Hall problem- a peek through simulation

I am taking this STATE-80 course from Harvard Extension School. This course teaches commonly used distributions and probability theory. The instructor Hatch is a really good teacher and he uses simulation for all the demonstrations along with the formulas. In week 6, we revisited the Monty Hall problem which we played on the first day of class. If you have not heard about it, I quoted from the wiki: Suppose you’re on a game show, and you’re given the choice of three doors: Behind one door is a car; behind the others, goats.

Modeling single cell RNAseq data with multinomial distribution

I was reading Feature Selection and Dimension Reduction for Single Cell RNA-Seq based on a Multinomial Model. In the paper, the authors model the scRNAseq counts using a multinomial distribution. I was using negative binomial distribution for modeling in my last post, so I asked the question on twitter: for modeling RNAseq counts, what’s the difference/advantages using negative binomial and multinomial distribution? — Ming Tang (@tangming2005) November 26, 2019 some quotes from the answers I get from Matthew