Tag: tSNE

Single-cell RNA-seq workflow

In this tutorial we walk through a typical single-cell RNA-seq analysis using Bioconductor packages. We will try to cover data from different protocols, but some of the EDA/QC steps will be focused on the 10X Genomics Chromium protocol. We start from the output of the Cell Ranger preprocessing software. This…

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How can i control the cluster number in scRNASeq clustering by Seurat package

How can i control the cluster number in scRNASeq clustering by Seurat package 2 Hi all, I analysised the 10x dataset by Seurat pkg, when i used the TSNEPlot function to plot the TSNE plot of clustering result, i found the number of cluster always different. How can i control…

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University of Connecticut Single Cell RNA-seq Workshop December 12-15, 2023

News:University of Connecticut Single Cell RNA-seq Workshop December 12-15, 2023 0 Join UConn’s Computational Biology Core for a Single Cell RNAseq Workshop December 12-15, 2023 Scope of the workshop: Introduction to different data file formats. Understanding the Considerations while designing single-cell RNA-seq experiments, Hands on steps to convert raw single-cell…

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Scanpy Pearson residual PCA error

Scanpy Pearson residual PCA error 2 I got a ValueError: Input contains NaN, infinity or a value too large for dtype(‘float32’). when trying to run this part of the code sc.pp.pca(adata, n_comps=50) n_cells = len(adata) sc.tl.tsne(adata, use_rep=”X_pca”) Not sure if the cause of error is becauseI I merge 4 10x…

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Optimized RT-qPCR and a novel normalization method for validating circulating miRNA biomarkers in ageing-related diseases

Reagents miRNeasy Serum/Plasma Advanced Kit (Qiagen, Hilden, Germany, # 217204); TaqMan® Advanced miRNA cDNA Synthesis Kit (Applied Biosystems, Bedford, MA, USA, #A28007); TaqMan® Fast Advanced Master Mix (Applied Biosystems, Bedford, MA, USA, # 4444556); TaqMan® Advanced miRNA Assays Single-tube assays (Applied Biosystems, Bedford, MA, USA, # A25576: 478293_mir, Spike-In cel-miR-39-3p;…

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Metaproteogenomic analysis of saliva samples from Parkinson’s disease patients with cognitive impairment

Characteristics of participants and analyses A total of 115 individuals (43 PDD, 45 PD-MCI) and 27 HC were included in this study. Both 16 S rRNA gene amplicon sequencing based microbiome analysis and metaproteomics profiling were performed for all salivary samples collected from the participants (Fig. 1). Fig. 1: Experimental overview….

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UMAP or TSNE for single cells?

UMAP or TSNE for single cells? 0 Dear all fellow, I am just slowly getting into single cells. I have been working with my data for 2.5 months now and tried to learn all the tips about single cell good practices. I personally find UMAP is tricky especially when we…

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python – How to use tensorboard Embedding Projector using Pytorch with custom dataset and custom model

Currently im doing image embedding visualisation and I want to use Tensorboard Projector PCA and T-SNE to see the image embedding similarity. I follow a website code to do the visualisation but I am unable to make the expected visualisation where the same images should clump together but it just…

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The Atoh1-Cre Knock-In Allele Ectopically Labels a Subpopulation of Amacrine Cells and Bipolar Cells in Mouse Retina

Abstract The retina has diverse neuronal cell types derived from a common pool of retinal progenitors. Many molecular drivers, mostly transcription factors, have been identified to promote different cell fates. In Drosophila, atonal is required for specifying photoreceptors. In mice, there are two closely related atonal homologs, Atoh1 and Atoh7….

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The urinary RNA atlas of patients with chronic kidney disease

Differential abundance analysis of urinary RNAs in CKD patients compared to healthy controls To explore the abundance of urinary RNAs, we performed an analysis using a dataset consisting of 80 CKD samples (GSE121978) and 47 healthy controls (GSE128359). This analysis encompassed a wide range of RNA types, including 36 circRNAs,…

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OmicsSuite: Tailored Pipeline for Multi-Omics Big Data Analysis

Abstract: With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems, however it is challenging…

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From counts or RPKM > PCA > tSNE visualization of PCA

single cell RNAseq: From counts or RPKM > PCA > tSNE visualization of PCA 2 Hello! I am a beginner at RNA seq analysis, I was hoping someone would point me in the direction of how I can take a data set (~50K genes in rows + 200 cells in…

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Feature plot not applicable for RunTSNE object in seurat?

Feature plot not applicable for RunTSNE object in seurat? 1 Dear All, I visualized my cluster using tsne object (image attached) and would like to run FeaturePlot to examine the expression of particular gene, but it did not work for tsne object. I could only do it with UMAP. Any…

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Filter, Plot, and Explore with Seurat in RStudio

First thing’s first, we need to load the packages we will be using. In order to use any functions of a package, we must first call the library of that package. In your console (likely in the lower left corner of your RStudio window), run the following lines of code…

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TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development

Curation of early-embryo development single-cell RNA-seq data sets for studying cell-cell communication To identify and study eLRs, we collected public early embryo development scRNA-seq datasets from the mouse MII-oocyte stage to the late blastocyst stage to ensure that scRNA-seq datasets represented every stage of early embryo development. In addition, to…

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t-SNE plot dots that are close together assigned to different clusters.

Hi, I have been having trouble to understand why some dots are so close together in t-SNE plot but they are assigned to different clusters in FindNeighbors() and FindClusters()? For example below plot: The most of the cluster 0 (red dots) are in bottom right but there are some are…

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Error in h(simpleError(msg, call)) in monocle2

Error in h(simpleError(msg, call)) in monocle2 0 Want to run monocle2 for a single cell RNAseq data processed using Seurat, but encountering following problem. library(monocle) Seurat An object of class Seurat 41445 features across 55683 samples within 1 assay Active assay: RNA (41445 features, 1850 variable features) 4 dimensional reductions…

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How to preprocess and visualize beautifully scRNA-seq with omicverse?

Omicverse is the fundamental package for multi omics included bulk and single cell RNA-seq analysis with Python. To get started with omicverse, check out the Installation and Tutorials. For more details about the omicverse framework, please check out our publication. The count table, a numeric matrix of genes\u2009\u00d7\u2009cells, is the…

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Day 17 Dimensionality Reduction by Muhammad Dawood

Python for Data Science Day 17: Dimensionality Reduction Welcome to Day 17 of our Python for data science challenge! Dimensionality Reduction is a powerful technique used to simplify high-dimensional data while preserving essential information. Today, we will explore dimensionality reduction techniques, including Principal Component Analysis (PCA) and t-distributed Stochastic Neighbor…

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new visualization method for dimension reduction technique

new visualization method for dimension reduction technique 0 Hello, I heard that there is a new dimension reduction technique that for visualization, and it better than UMAP and TSNE. However, anyone heard about this new technique? And how is it performance? ThanksAndy dimension-reduction • 38 views • link updated 40…

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Bioconductor – esetVis

DOI: 10.18129/B9.bioc.esetVis     Visualizations of expressionSet Bioconductor object Bioconductor version: Release (3.5) Utility functions for visualization of expressionSet (or SummarizedExperiment) Bioconductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available. Author: Laure Cougnaud…

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An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis | Malaria Journal

Optimization of the pipeline on monoclonal and simulated mixed infection samples Towards optimizing GATK4 for P. falciparum, the creation of an improved training “truth set” for the pipeline was key. To filter raw VCFs with a high quality truth callset, which is difficult to obtain using wet laboratory methods, a…

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Staff Bioinformatics Scientist – San Leandro

Bioinformatics Scientist We are seeking a highly motivated and skilled Bioinformatics Scientist to join our R&D team. The successful candidate will be integral to our genomics research efforts. This role requires expertise building pipelines from sequencer output to feature generation from both RNA and DNA sources. The candidate should have…

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Should primary tumor RNA-Seq match their derived cell lines and PDXs? And which dimensionality reduction method should I use?

Should primary tumor RNA-Seq match their derived cell lines and PDXs? And which dimensionality reduction method should I use? 0 I have processed a bunch of RNA-Seq data coming from patient primary tumours and their respective established cell lines and PDXs. My question is, should the cell lines/PDXs cluster together…

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Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain

Analysis overview This manuscript reports the collective efforts from the teams that participated in the SpaceJam Hackathon (spacetx.github.io/spacejam.html) organized by the SpaceTx Consortium. We explored multiple approaches to assign the spatial data with reference scRNA-seq cell type annotations and developed meta-analysis strategies to combine the cell type assignment results from…

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CIBERSORTx hires mode duplicates

CIBERSORTx hires mode duplicates 0 I recently ran a CIBERSORTx hires run where the output file for one of the cell types (e.g., monocytes) had a few genes with the same expression value across all samples. I was wondering why this was the case and that I should remove them…

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Single-cell RNA sequencing reveals the fragility of male spermatogenic cells to Zika virus-induced complement activation

Cell clusters in ZIKV-infected mouse testis defined by scRNA-Seq To investigate the influence of ZIKV infection on testes, testicular cells from ZIKV-infected (14 dpi.) and uninfected A6 male mice (Ifnar−/− mice) were analyzed by single-cell RNA sequencing (scRNA-Seq). After filtering out poor-quality cells, 11014 cells in control testes and 11974…

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How do I project known tSNE coordinates onto SeuratObject

How do I project known tSNE coordinates onto SeuratObject 1 I would like to analyze a published scRNAseq dataset by making a new Seurat Object. The authors have published their tSNE.1 and tSNE.2 coordinates in addition to all of their metadata but I cannot find how to create a tSNE…

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Domain adaptation for supervised integration of scRNA-seq data

SIDA framework To achieve supervised integration, we propose to use a domain adaptation deep learning network architecture, which is able to incorporate cell type labels to inform data integration. As shown in Fig. 1, this network architecture takes training pairs generated by cells from different batches as input and passes the…

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Virtual Single Cell RNA-seq Workshop

The Computational Biology Core at the University of Connecticut’s Institute for Systems Genomics is offering a virtual Single Cell RNA-seq workshop March 20-23, 2023. The workshop will be run on a high performance computing cluster, and cover the basics of Linux and writing/submitting scripts. The goal is to familiarize attendees…

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CyTOF FlowCore Catalyst Question

CyTOF FlowCore Catalyst Question 0 Hi. Thank you in advance. I analyze my flow, actually CyTOF, files (fcs) using R vignettes from Malgorzata Nowicka, eta al. CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets (F1000 article f1000research.com/articles/6-748/v3). Everything works great. I have multiple samples from two groups (condition) and…

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rna seq – How will Seurat handle pre-normalized and pre-scaled data?

I don’t do transcriptome analysis, it ain’t my thing, however I do understand statistical analysis as well as the underlying issue regarding the public availability of molecular data … I agree with the OP its not ideal. However, yes the OP can continue with ‘clustering’, personally I definitely prefer it…

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One-step induction of photoreceptor-like cells from human iPSCs by delivering transcription factors

Introduction of CRX and NEUROD1 using piggyBac vector into iPSCs and differentiation to induced photoreceptor-like cells (iPRCs) (A) Design of polycistronic piggyBac vector for CRX and NEUROD1 mediated conversion under control of the tetracycline operator rtTA and neomycin resistance gene. Dox: doxycycline, rtTA: reverse tetracycline transactivator, neo: neomycin resistance gene….

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scrnaseq – Arrange ggplot Figure for scRNA-seq data

I have generated a ggplot for 8 single-cell libraries, with the purpose of visualizing the tSNE facet plot by sample, colored by cell type — with percentages. The best I could get to is this – however, it looks too crowded, and I also want the cell types to be…

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Labeling Clusters in ggplot

Labeling Clusters in ggplot 1 I have a data matrix I extracted from seurat and I want to plot the tSNE plot by using ggplot. I don’t know how to label the clusters on the plot with 0..15. Help is appreciated. ggplot single cell • 1.3k views This is what…

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tSNE and UMAP of scATAC-seq data looks like spaghetti

tSNE and UMAP of scATAC-seq data looks like spaghetti 0 I would like to use R to generate cluster my 20k cells from a single cell ATAC-seq experiment. I ran PCA then selected the first 50 components, which were put into tSNE’s normalize_input() then Rtsne(). This is the result I…

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A question about scRNA-seq analysis

A question about scRNA-seq analysis 0 Dear all, please may I ask for a suggestion : I have a scRNA-seq dataset, which has 2 groups (Control and Model). I would like to process all the samples into cluster by tSNE or UMAP , then classification or differentiation the cell types….

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How to display TCR data in tsne space via seurat object

How to display TCR data in tsne space via seurat object 1 Hi Guys, I am trying to work out how I can display by VDJ usage within my tsne plot for some 10x data. I added everything to the Seurat object and tried to do a feature plot to…

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