English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

Gene expression in individual cells can now be measured for thousands of cells in a single experiment thanks to innovative sample-preparation and sequencing technologies. State-of-the-art computational pipelines for single-cell RNA-sequencing data, however, still employ computational methods that were developed for traditional bulk RNA-sequencing data, thus not accounting for the peculiarities of single-cell data, such as sparseness and zero-inflated counts. Here, we present a ready-to-use pipeline named  gf-icf  (gene frequency–inverse cell frequency) for normalization of raw counts, feature selection, and dimensionality reduction of scRNA-seq data for their visualization and subsequent analyses. Our work is based on a data transformation model named term frequency–inverse document frequency (TF-IDF), which has been extensively used in the field of text mining where extremely sparse and zero-inflated data are common. Using benchmark scRNA-seq datasets, we show that the  gf-icf  pipeline outperforms existing state-of-the-art methods in terms of improved visualization and ability to separate and distinguish different cell types.

A Tool for Visualization and Analysis of Single-Cell RNA-Seq Data Based on Text Mining