Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types

Hi all, I wrote this tutorial

https://divingintogeneticsandgenomics.com/post/how-to-convert-raw-counts-to-tpm-for-tcga-data-and-make-a-heatmap-across-cancer-types/

Hope it is useful!

Happy Learning! Tommy

rnaseq heatmap rstats tcga

• 1,140 views • link

written 2.8 years ago by Ming Tommy Tang

0 answers

No answers yet.

More posts like this

Tutorial: How to calculate partial correlation controlling cancer types
written 1.2 years ago by Ming Tommy Tang

Hello Biostars, I just wrote this tutorial on how to calculate partial correlation. https://divingintogeneticsandgenomics.com/post/partial-cor/ It was for my understanding of using linear models to calculate …
Tutorial: PCA analysis on TCGA bulk RNAseq data
written 1.5 years ago by Ming Tommy Tang

Hello Bioinformatics lovers, I wrote a tutorial on how to download TCGA RNAseq count data and make a PCA and heatmap with it. https://divingintogeneticsandgenomics.com/post/pca-tcga/ Enjoy! …
Tutorial: How CCA alignment and cell label transfer work in Seurat
written 1.8 years ago by Ming Tommy Tang

Hi Bioinformatics lovers, I have another blog post out on understanding CCA alignment and cell label transfer work in Seurat at a low level https://divingintogeneticsandgenomics.com/post/cca-alignment/ …
Blog: How Seurat PCA projection, KNN and MNN for label transfer work
written 1.8 years ago by Ming Tommy Tang

Hello, I wrote this blog post to understand how PCA projection, KNN and MNN work in Seurat for single-cell label transfer work. https://divingintogeneticsandgenomics.com/post/pca-projection/ Enjoy! Tommy
Tutorial: 4 CITE-seq tutorials
written 2.6 years ago by Ming Tommy Tang

Hi Bioinformatics lovers, I put together 4 blog posts on CITE-seq analysis: Part 1 How to use Salmon/Alevin to preprocess CITE-seq data https://divingintogeneticsandgenomics.com/post/how-to-use-salmon-alevin-to-preprocess-cite-seq-data/ Part 2 …
Tutorial: CITEseq tutorial
written 2.7 years ago by Ming Tommy Tang

Hi, I wrote two tutorials on CITE-seq analysis: 1. How to use Salmon/Alevin to preprocess CITE-seq data https://divingintogeneticsandgenomics.com/post/how-to-use-salmon-alevin-to-preprocess-cite-seq-data/ 2. CITE-seq downstream analysis: From Alevin output …
Blog: How to use random forest for clustering
written 2.7 years ago by Ming Tommy Tang

Hi all, I just wrote this blog post showing how to use random forest as a clustering method. https://divingintogeneticsandgenomics.com/post/use-random-forest-as-a-clustering-method/ Enjoy! Tommy
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
written 3.0 years ago by Ming Tommy Tang

Hi all, I just wrote a blog post on multiomics data integration. https://divingintogeneticsandgenomics.com/post/multi-omics-data-integration-a-case-study-with-transcriptomics-and-genomics-mutation-data/ Happy Learning! Tommy
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
written 3.0 years ago by Ming Tommy Tang

Hi all, I've written a tutorial on how to do niche analysis for spatial data https://divingintogeneticsandgenomics.com/post/neighborhood-cellular-niches-analysis-with-spatial-transcriptome-data-in-seurat-and-bioconductor/ Happy Learning! Tommy
Tutorial: best practices for single-cell RNAseq analysis
written 3.1 years ago by Ming Tommy Tang

Hi all, I recently gave a talk on this topic and hope it is useful for you https://www.youtube.com/watch?v=fDz1lJ2el08 The slides can be found at https://divingintogeneticsandgenomics.com/talk/2023-poland/ …