Tutorial: How to pre-process scRNAseq data from fastq to count matrix with two lines of code

Hi!

I just made this video.

and find the script at https://github.com/crazyhottommy/compbio_tutorials/blob/main/scripts/06_scRNseq_two_lines_from_fastq_to_count_matrix.Rmd

Happy learning!

Tommy

unix scrna-seq single-cell rstats

• 1,334 views • link

updated 3.1 years ago by Ram

• written 3.1 years ago by Ming Tommy Tang

0 answers

No answers yet.

More posts like this

Tutorial: SingleCellExperiment object explained with a real-world example
written 2.2 years ago by Ming Tommy Tang

Hi all, I made a tutorial explaining what is SingleCellExperiment object and use an example you can follow. Script: https://github.com/crazyhottommy/compbio_tutorials/blob/main/scripts/08_intro_to_singleCellExperiment.Rmd Video: https://www.youtube.com/watch?v=eTzh6iWPqeQ Happy Learning! Tommy
Tutorial: How to Use Biomart to Find Mouse Orthologs for Human Genes
written 2.6 years ago by Ming Tommy Tang

Hello! The code can be found at https://github.com/crazyhottommy/compbio_tutorials/blob/main/scripts/R_tips_09_biomart_mouse_ortholog.Rmd I also made a video https://www.youtube.com/watch?v=sQFEE_EZIgQ Happy Learning! Tommy
Tutorial: download metadata using GEOquery
written 2.7 years ago by Ming Tommy Tang

Hi, I made this video showing you how to download metadata from GEO using GEOquery. https://www.youtube.com/watch?v=NSoU58IqA3Y The script can be found at https://github.com/crazyhottommy/compbio_tutorials/blob/main/scripts/15_how_to_get_metadata_GEO.Rmd Happy Learning! …
Tutorial: How to convert gene ids in R
written 3.1 years ago by Ming Tommy Tang

Hi all, I made this video: https://www.youtube.com/watch?v=OMm6Db6dsiM Download the script at https://github.com/crazyhottommy/compbio_tutorials/blob/main/scripts/R_tips_08_convert_gene_ids.Rmd Happy Learning! Tommy
Tutorial: How to read multiple matrices from GEO into R and make multiple Seurat objects and merge …
written 3.1 years ago by Ming Tommy Tang

Hi, I saw people asking this question, so I made a video. https://www.youtube.com/watch?v=5e_8wr5Xx_Q Download the script at https://github.com/crazyhottommy/compbio_tutorials/blob/main/scripts/04_create_seurat_object_from_GEO.Rmd Happy Learning! Tommy
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
written 3.1 years ago by Ming Tommy Tang

Hi all, I made this video to explain hierarchical clustering in R. https://www.youtube.com/watch?v=KPtucxQC5ew Download the script at https://github.com/crazyhottommy/compbio_tutorials/blob/main/scripts/R_tips_06_hierarchical_clustering.Rmd Happy Learning! Tommy
Tutorial: How to do GSEA in R for RNAseq data
written 3.1 years ago by Ming Tommy Tang

Hi, I made this video to show you how to do GSEA in R and understand the GSEA plot https://www.youtube.com/watch?v=IKCDQEpuJDA The R script is at …
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
written 3.1 years ago by Ming Tommy Tang

Hi all, I made this video to show you how to merge all the count tables into a single dataframe https://www.youtube.com/watch?v=rdbPNYg4g4k Download the script at …
Tutorial: How to make a perfect heatmap using RNAseq data
written 3.1 years ago by Ming Tommy Tang

Hi all, Please find this video tutorial https://www.youtube.com/watch?v=LmZD_a8XZEQ and the Rmarkdown file at https://github.com/crazyhottommy/compbio_tutorials/blob/main/scripts/02_differential_expression_heatmap.Rmd Happy Learning! Tommy
Tutorial: How to make a heatmap in R and deep understand it
written 3.3 years ago by Ming Tommy Tang

Hi all, I made a video on making heatmap with R and how to understand it deeply https://www.youtube.com/watch?v=7fQkPUqusTg&t=1s The Rmarkdown file https://github.com/crazyhottommy/compbio_tutorials/blob/main/scripts/01_how_to_make_a_heatmap.Rmd If you use …