Cancer immunotherapy targeting co-inhibitory pathways by checkpoint blockade shows remarkable efficacy in a variety of cancer types. However, only a minority of patients respond to treatment due to the stochastic heterogeneity of tumor microenvironment...
Read More »Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis
Single-cell RNA-sequencing (scRNA-Seq) is a compelling approach to directly and simultaneously measure cellular composition and state, which can otherwise only be estimated by applying deconvolution methods to bulk RNA-Seq estimates. However, it has not yet become a widely used tool ...
Read More »TransSynW – A single‐cell RNA‐sequencing based web application to guide cell conversion experiments
Generation of desired cell types by cell conversion remains a challenge. In particular, derivation of novel cell subtypes identified by single‐cell technologies will open up new strategies for cell therapies. The recent increase in the generation of single‐cell RNA‐sequencing (scRNA‐seq) ...
Read More »Spectacle – an interactive resource for ocular single-cell RNA sequencing data analysis
Single-cell RNA sequencing has revolutionized ocular gene expression studies. This technology has enabled researchers to identify expression signatures for rare cell types and characterize how gene expression changes across biological conditions...
Read More »cellxgene VIP – a web-based tool for the exploration and visualization of scRNA-seq data
Among few scRNA-seq data visualization tools evaluated in a recent publication, cellxgene developed by Chan Zuckerberg Initiative is highly recommended because of its scalability and interactivity, which is also adopted by many Human Cell Atlas projects. However, after implemented in ...
Read More »Multi-omic data and interactive web tool made publicly available to aid COVID-19 research
Why is it that some COVID-19 patients become extremely ill and die, while others experience only mild symptoms? The molecular underpinnings of...
Read More »deepTS – exploring transcriptional switches from pairwise, temporal and population RNA-Seq data
Transcriptional switch (TS) is a widely observed phenomenon caused by changes in the relative expression of transcripts from the same gene, in spatial, temporal or other dimensions. TS has been associated with human diseases, plant development...
Read More »Ribotoolkit – an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution
Ribosome profiling (Ribo-seq) is a powerful technology for globally monitoring RNA translation; ranging from codon occupancy profiling, identification of actively translated open reading frames (ORFs), to the quantification of translational efficiency under...
Read More »IRIS3 – integrated cell-type-specific regulon inference server from single-cell RNA-Seq
A group of genes controlled as a unit, usually by the same repressor or activator gene, is known as a regulon. The ability to identify active regulons...
Read More »fRNAkenseq – a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool
Decreasing costs make RNA sequencing technologies increasingly affordable for biologists. However, many researchers who can now afford sequencing lack...
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