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The momentum of scRNA-seq datasets prompts for simple and powerful tools exploring their meaningful signatures. Here we present Single-Cell_Signature_Explorer (https://sites.google.com/site/fredsoftwares/products/single-cell-signature-explorer), the first method for qualitative and high-throughput scoring of any gene set-based signature at the single cell level and its visualization using t-SNE or UMAP. By scanning datasets for single or combined signatures, it rapidly maps any multi-gene feature, exemplified here with signatures of cell lineages, biological hallmarks and metabolic pathways in large scRNAseq datasets of human PBMC, melanoma, lung cancer and adult testis.
This article was published in the following journal.
Name: Nucleic acids research
Identification of human disease signature genes typically requires samples from many donors to achieve statistical significance. Here, we show that single-cell heterogeneity analysis may overcome this...
Single-cell technologies have emerged as advanced tools to study various biological processes that demand the single cell resolution. To detect subtle heterogeneity in the transcriptome, high accuracy...
Transcriptomics has been revolutionized by massive throughput RNA-seq. To date, the ongoing decrease in sequencing cost and recent eruption of single-cell related protocols have boosted a demand for s...
In recent years, single-cell RNA sequencing enables us to discover cell types or even subtypes. Its increasing availability provides opportunities to identify cell populations from single-cell RNA-seq...
Hepatocellular carcinoma (HCC) is heterogeneous, rendering its current curative treatments ineffective. The emergence of single-cell genomics represents a powerful strategy in delineating the complex ...
Preimplantation genetic diagnosis (PGD) is the integration of both assisted reproductive technologies and molecular genetic technologies and was shown to improve implantation rate and redu...
The primary aim of the study is to identify a predictive molecular signature for response to chemotherapy, according to WHO criteria, in patients with non-small cell lung cancer by studyin...
This is a single center, single arm, open-lable phase I study to determine the safety and efficacy of CD19-STAR-T cells in patients with refractory and relapsed B-cell malignancies (such a...
This is a single-center, open-label, single-arm study to evaluate the safety and efficacy of anti-CD22 CAR-T cells in patients with relapsed or refractory B-cell Malignancies.
This is a single center, single arm, open-lable phase I study to determine the safety and efficacy of CD19-CAR-T cells in patients with refractory and relapsed B-cell malignancies.
A genotoxicological technique for measuring DNA damage in an individual cell using single-cell gel electrophoresis. Cell DNA fragments assume a "comet with tail" formation on electrophoresis and are detected with an image analysis system. Alkaline assay conditions facilitate sensitive detection of single-strand damage.
The movement of CYTOPLASM within a CELL. It serves as an internal transport system for moving essential substances throughout the cell, and in single-celled organisms, such as the AMOEBA, it is responsible for the movement (CELL MOVEMENT) of the entire cell.
Assaying the products of or monitoring various biochemical processes and reactions in an individual cell.
A genus of RED ALGAE in the family Porphyridiaceae. A single stellate CHLOROPLAST is present in each cell which has no CELL WALL.
Mapping of the full chromosome set of the nucleus of a cell. The chromosome characteristics of an individual or a cell line are usually presented as a systematized array of metaphase chromosomes from a photomicrograph of a single cell nucleus arranged in pairs in descending order of size and according to the position of the centromere. (From Stedman, 25th ed)
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...
Biological therapy involves the use of living organisms, substances derived from living organisms, or laboratory-produced versions of such substances to treat disease. Some biological therapies for cancer use vaccines or bacteria to stimulate the body&rs...