Tag: SmartSeq

Hi! I have smartseq2 RPKM data (already analysed with Seurat pipeline) and I want to do trajectory analysis of my cells. Having RPKM data I wondered whether I can use Monocle 3 or can it just be used with UMI data (10x) ? In Monocle2 it seemed to be possible…

Recommended way to normalize SmartSeq2 gene expression matrix to better match 10X expression data 0 Hi, I have single-cell RNA sequencing data from similar tissue, one dataset collected with SmartSeq2 (full transcript length, no UMIs), and another dataset collected from 10X (3′ end, with UMIs). I am doing a standard…

Single Cell Pipeline for SmartSeq 1 Dear Community, I want to align SmartSeq platform-based single-cell data to the human genome using Alevin and/or StarSolo and then create a Seurat object. My data is paired-end. Each FASTQ file is around 4-10 GB in size. R1 and R2 pairs look like this:…

Login and apply Do you want to contribute to improving human health”strong Please join Dr. Bj?rkegren’s team of world-leading bioinformaticians working across the globe in Mount Sinai Hospital in New York to Karolinska Institutet in Sweden and Tartu University Hospital in Estonian. Our main source of systems genetics analyses is…

DOI: 10.18129/B9.bioc.MouseThymusAgeing     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MouseThymusAgeing. Single-cell Transcriptomics Data of the Ageing Mouse Thymus Bioconductor version: 3.13 This package provides data access to counts matrices and meta-data for single-cell RNA sequencing data of thymic epithlial cells…

Do you want to contribute to improving human health? Please join my team of world-leading bioinformaticians working across the globe in Mount Sinai Hospital in New York to Karolinska Institutet in Sweden and Tartu University Hospital in Estonian. Our main source of systems genetics analyses is the cardiovascular disease (CVD)…

seurat v3 object ASSAYS: RNA: mRNA expression data DIMENSIONALITY REDUCTION projected: Data was projected on the main AML dataset from Cohorts A and B. scanorama: Data was integrated with Scanorama, using the patient as Batch key umap: umap computed from Scanorama components METADATA patient: Patient ct: Projected cell type (Triana…

Introduction Single cell RNA-seq (scRNA-seq) is a powerful tool to measure gene expression in individual cells. While relative gene expression differences are currently analyzed with great interest in single cell data, differences in total transcript levels were mainly considered technical artefacts and removed during normalization, assuming that single cells contain…

I’m a data scientist trying to branch out into more bioinformatics/genetics. My tutorial is counting spike-ins, but his explanation was over my head: 1 – AnnData and Preprocessing spike-ins | Kaggle ” Because this is smartseq2 data, we may have spike-ins. An RNA spike-in is an RNA transcript of known…

Re-analysis of multiple scRNAseq data as a combined new one 0 Hi all, There are so many regions in brain.The cortex itself is of many types.I found many single cell RNA seq studies which focus on different regions eg- gse … somatosensory cortex dropseq year 2015 gse….. primary visual cortex…

Forum:Differences between SMART-seq2, SMART-seq3, and 10x 0 Hi everyone, I’ve recently started analyzing single-cell RNA-seq data (with FASTQ files as a starting point) and so far I have used 10x genomics data from their website. Now, I’m interested in using data generated by other protocols, specifically SMART, because it is…

SmartSeq vs SmartSeq2 0 My data is SmartSeq data, and I would like to run the velocyto command for SmartSeq2 to carry out the initial conversion step for RNA velocity analysis. My question is quite simple: what is the difference between smartseq and smartseq2? Is this difference large enough to…