Single cell RNA-seq data clustering using TF-IDF based methods
Related Experiment Video
Updated: Feb 3, 2026
Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq
Published on: August 25, 2020
Marmar Moussa1, Ion I Măndoiu2
1University of Connecticut, Storrs, 06269, CT, USA.
Background:
Single cell transcriptomics is critical for understanding cellular heterogeneity and identification of novel cell types. Leveraging the recent advances in single cell RNA sequencing (scRNA-Seq) technology requires novel unsupervised clustering algorithms that are robust to high levels of technical and biological noise and scale to datasets of millions of cells.
Results:
We present novel computational approaches for clustering scRNA-seq data based on the Term Frequency - Inverse Document Frequency (TF-IDF) transformation that has been successfully used in the field of text analysis.
Conclusions:
Empirical experimental results show that TF-IDF methods consistently outperform commonly used scRNA-Seq clustering approaches.
Related Concept Videos
03:21RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
01:20Cluster Sampling Method
To choose a cluster sample, divide the population into clusters (groups) and then randomly select some of the clusters. All the members from these clusters are in the cluster sample. For example, if you randomly sample four departments from your...
01:23RNA Structure
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
01:25Statistical Methods for Analyzing Epidemiological Data
02:53Ribosomal RNA Synthesis
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
01:53RNA Stability