Tag: scRNA

Terminator Upgrades Single-Cell RNA Sequencing Technology

Japanese scientists have developed a new method for DNA amplification and sequencing that improves the accuracy of single-cell RNA sequencing (scRNA-seq). The new method called TAS-Seq uses a terminal transferase enzyme that amplifies and sequences DNA complementary to mRNA (cDNA) in solid phase on a nanowell/magnetic bead-based cell isolation platform….

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A*STAR RESEARCH ENTITIES hiring #SGUnitedJobs Bioinformatics Specialist, Lab of Cancer Epigenetic Regulation, GIS in Singapore, Singapore

The Laboratory of Cancer Epigenetic Regulation, helmed by GIS Executive Director Patrick Tan, is seeking a Bioinformatician to join a new multi-institutional effort targeting the genetic basis of cancer to create novel therapies and diagnostics. Led by an award-winning thought leader in the field of Asian gastrointestinal cancer research with…

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What counts as a valid biological replicate in single cell RNAseq?

Forum:What counts as a valid biological replicate in single cell RNAseq? 3 I’ve run an experiment where I collected orans from 3x healthy control mice, and 3x post-injury mice – and ended up generating around 3000 individual single cells from each sample. For consistency and cost reasons, we pooled our…

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GeneActivity without Fragments file in Seurat for Integrating scRNA-seq and scATAC-seq

Hi all, I am new to R and Seurat, and I am following Seurat tutorials to find anchors between RNA-seq and ATAC-seq data according to: Combining the two tutorials is difficult for a cell line data set I am using for SNARE-seq Human here. I managed to run the following…

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GENCODE – Human Release 32 Statistics

Statistics about the GENCODE Release 32 The statistics derive from the gtf file that contains only the annotation of the main chromosomes. For details about the calculation of these statistics please see the README_stats.txt file. General stats Total No of Genes 60609 Protein-coding genes 19965 Long non-coding RNA genes 17910…

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Single-Cell Transcriptome Resource From Human Cell Atlas Team Yields Immune, Disease Insights

NEW YORK – A large international team came up with single-cell and single-nucleus transcriptomic resources to characterize the diverse cell types found in the human body, along with related gene expression and splicing features that offer clues to processes at play within and across tissues and organs. In a series…

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Strange Per base sequence content of fastqc

Hi, all! I download fastq.gz files of GSE162708 from ENA which only have 2 files of each sample(usually scRNA-seq has 3 files I1 , R1 & R2 ). Then I run fastp as following Then I get QC report , but I can’t understand why Per base sequence content of…

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Quantification of similarity between scRNA-seq datasets? : bioinformatics

I’m using a mouse model which has been used in a couple previous scRNA-seq studies, but I’ve added a novel treatment. I’m trying to determine the similarity between these previous studies and mine to determine how much our treatment affected the cell states. I am not looking to integrate the…

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How can I validate the results by the software package, I have recently developed using python for genomic data?

How can I validate the results by the software package, I have recently developed using python for genomic data? 1 I have developed a software package for the analysis of genomic data, in which, I have implemented a variety of functions like normalization, clustering etc (from already available tools i.e.,…

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Single cell database scrna dB for bioinformatics database development (1)

Single cell database construction High quality integrated single cell database If readers just want to get a ready-made single-cell database with rich content and add it to their own PC or linux The server , You can skip the following detailed theoretical tutorial Database download link : Click to download…

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How to use MARS-seq dataset for 10X scRNA-seq cluster annotation (i.e. convert the dataset to Seurat object)

How to use MARS-seq dataset for 10X scRNA-seq cluster annotation (i.e. convert the dataset to Seurat object) 0 Hi, I am new to single-cell sequencing analysis. I performed 10x scRNA-seq and found the only suitable research paper on single-cell sequencing of the same tissue site. But their single-cell sequencing uses…

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scrnaseq – Normalization methods to combine scRNA-seq experiments with different sequencing depths

I don’t think you need to complicate the idea of normalisation by introducing machine learning classifiers as a necessary component. Normalisation is common when comparing different datasets for all differential analysis. If you have single cell data, have a look at integration techniques in the Seurat workflows: satijalab.org/seurat/articles/integration_rpca.html If you’ve…

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scrnaseq – What are methods to measure scRNA-seq data complexity?

There are some scRNA-seq data sets which cluster very easily in good accordance to ground truth cell type, and there are those that do not because of higher complexity. Things make the data complex I think are the presence of rare cells and a good deal of apparent mixing between…

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Absolute Scaling of Single-Cell Transcriptomes Reveals Pervasive Hypertranscription in Adult Stem and Progenitor Cells

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…

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How to identify and compare cell-type signatures between two scRNA-seq datasets? : bioinformatics

Hi all. I just started a new research job and am going through a learning curve at the moment. For my research, I’m comparing mouse scRNA-seq data from femur and skull bone marrow. I’m particularly interested in the different macrophage markers/signatures that are present in each dataset. How do I…

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DataViz question for DEG and scRNA-seq

DataViz question for DEG and scRNA-seq 1 Maybe a dumb question, but I recently came across a single-cell paper that showed “volcano” plots for all clusters in one image by filtering for all genes that were FDR <0.05, the x-axis being represented by different colors characterizing different clusters, the y-axis…

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A single-cell atlas of human and mouse white adipose tissue

Rosen, E. D. & Spiegelman, B. M. What we talk about when we talk about fat. Cell 156, 20–44 (2014). CAS  PubMed  PubMed Central  Google Scholar  Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006)….

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Why do UMAP on all scRNA-seq samples rather than a UMAP for each treatment?

Why do UMAP on all scRNA-seq samples rather than a UMAP for each treatment? 1 When analyzing scRNA-seq data, why do people pool all their data across treatments and run UMAP on the combined dataset rather than running a separate UMAP on each treatment group? For example, say you’re looking…

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Research Associate job with KINGS COLLEGE LONDON

Job description A Postdoctoral Research Associate (PDRA) – Computational biology position is available in the Centre for Gene Therapy and Regenerative Medicine, King’s College London. This is an exciting opportunity to join an interdisciplinary team of scientists working on a Wellcome Trust funded research programme aimed at studying the mammalian…

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Bioconductor – TAPseq

DOI: 10.18129/B9.bioc.TAPseq     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TAPseq. Targeted scRNA-seq primer design for TAP-seq Bioconductor version: 3.12 Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using…

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Research Assistant, CSCB,LWK job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The SingHealth Duke-NUS Genomic Medicine Centre was established by SingHealth and Duke-NUS Medical School to advance the delivery of genomic medicine across the SingHealth Duke-NUS Academic Medical Centre (AMC). The Centre will bring together expertise from the various SingHealth institutions and Duke-NUS to leverage on advanced genomic technologies…

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Science Papers on Spatial Characterization of Sensory Neurons, Megakaryocyte Differentiation Mapping

A spatial transcriptomic analysis of key human sensory neurons is presented in Science Translational Medicine this week, uncovering potential new drug targets for pain management. Despite the significant medical problem pain represents, there has been little progress translating preclinical work on peripheral pain mechanisms, which has largely been done in rodents,…

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Boosting the efficiency of single-cell RNA sequencing — ScienceDaily

Single-cell RNA sequencing, or “scRNA-seq” for short, is a technique that allows scientists to study the expression of genes in an individual cell within a mixed population — which is virtually how all cells exist in the body’s tissues. Part of a larger family of “single-cell sequencing” techniques, scRNA-seq involves…

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The Difference Between Genome Reference(scRNAseq) And Transcriptome Reference(bulk RNAseq)

I want to know the difference between Genome Reference in scRNAseq and transcriptome reference in bulk RNAseq. But I didn’t get any better answer in any other place. I know we could download genome reference from UCSC, NCBI, ENSEMBL and GENECODE for bulk RNAseq. And here are the links below:…

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Novel CRISPR platform to decode the immune system

Date: 11th February 2022 The immune system is a critical biological network of processes that protects an organism from disease, and depends on the ability to distinguish self from non-self, a role driven by antigens.  In humans, T cells respond to antigen stimulation together with the production of cytokines however,…

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HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads

Reviewer #1 (Public Review): Droplet-based single-cell method development has stalled in the past years. The field has been overtaken by commercial solutions that optimized performance, but at much higher costs and without any possibility for customization. More recently, combinatorial indexing methods (e.g. SPLIT-seq) have gained popularity, requiring no specialized equipment…

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Postdoctoral position in bioinformatics – focused on single-cell immune transcriptomics – Karolinska Institute – job portal

Postdoctoral position in bioinformatics – focused on single-cell immune transcriptomics Login and apply Do you want to contribute to improving human health? We are looking for an ambitious postdoctoral fellow with solid genome-wide bioinformatics and computational biology skills to join our highly accomplished team. We offer a stimulating environment in…

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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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Spatial components of molecular tissue biology

1. Okabe, Y. & Medzhitov, R. Tissue biology perspective on macrophages. Nat. Immunol. 17, 9–17 (2016). CAS PubMed  Google Scholar  2. Xia, C., Fan, J., Emanuel, G., Hao, J. & Zhuang, X. Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc. Natl Acad. Sci. USA…

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Novel CRISPR Tool Activates Instead of Editing Human Immune Cell Genes

Scientists at Gladstone Institutes and UC San Francisco (UCSF) say they have co-opted the CRISPR-Cas9 system to forcibly activate genes—rather than edit them—in human immune cells. The method, known as CRISPRa, lets them discover genes that play a role in immune cell biology more thoroughly and rapidly than previously possible,…

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Scipio Bioscience Bets on Hydrogel Tech to Differentiate New Single-Cell RNA-seq Kit

NEW YORK – Paris-based Scipio Bioscience this week announced the European launch of its Asteria hydrogel-based single-cell RNA-seq kit. With less reliance on equipment and reagents, the RNA-seq library preparation kit provides researchers with a flexible benchtop protocol for labeling, isolating, and lysing cells, and recovering labeled mRNA. The Asteria kit comes…

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scrnaseq – Integrating scRNA-seq data using raw data

I believe when you say alignment, you mean aligning reads to a genome (sometimes to transcriptome) and count these to get count matrices. In the aforementioned paper, however, what is meant is “bringing different data sets to a level where they can be compared/integrated/…”. Basically scRNA-seq data are heavily prone…

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Which method works best for analysing ONE sample of scRNA-seq data?

Which method works best for analysing ONE sample of scRNA-seq data? 1 Hello, I currently have a single-cell RNA-seq (scRNA-seq) data of a single person (sample) and i want to perform DE analysis. However, when I run the DESeq() in the DESeq2 package, it shows an error about only one…

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Identification of a regulatory pathway inhibiting adipogenesis via RSPO2

Integration of APC scRNA-seq data reveals heterogeneity of adipocyte progenitor cells In a previous study9, we defined Lin−Sca1+CD142+ APCs as adipogenesis regulatory (Areg) cells and demonstrated that these cells are both refractory toward adipogenesis and control adipocyte formation of APCs through paracrine signaling. In contrast, Merrick et. al.4 observed that Lin−CD142+ cells…

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The Evolution of scRNA-seq Analysis

By Jane CookNovember 29, 2021 What Can scRNA-seq Data Tell Us? Single cell sequencing technologies have exploded in popularity for biological research over the last five years. The appeal of scRNA-seq lies in its specificity and scalability compared to older research techniques like Western blotting. Researchers can use scRNA-seq to…

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Decoding gene regulation in the fly brain

1. Li, H. et al. Classifying Drosophila olfactory projection neuron subtypes by single-cell RNA sequencing. Cell 171, 1206–1220 (2017). CAS  PubMed  PubMed Central  Google Scholar  2. Davie, K. et al. A single-cell transcriptome atlas of the aging Drosophila brain. Cell 174, 982–998 (2018). CAS  PubMed  PubMed Central  Google Scholar  3….

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Postdoctoral Scholar – Bioinformatics/Biomedical Data Science

The University of Nevada, Reno (UNR) appreciates your interest in employment at our growing institution. We want your application process to go smoothly and quickly. Final applications must be submitted prior to the close of the recruitment. If you need assistance or have questions regarding the application process, please contact…

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Postdoc Position in Bioinformatics in Stem Cell Neurobiology

DepartmentDepartment of Histology and Embryology  – Faculty of MedicineDeadline 28 Feb 2022Start date Jully 2022Job type full-timeJob field Science and research Medical Faculty of Masaryk University, Brno, Czech Republic, invites excellent scientists to apply for Postdoc position in Bioinformatics in Stem Cell Neurobiology   Description: The Department of Histology and Embryology is…

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Postdoc Position in Bioinformatics in Stem Cell Neurobiology job with MASARYK UNIVERSITY

Department Department of Histology and Embryology – Faculty of Medicine Deadline 28 Feb 2022 Start date Jully 2022 Job type full-time Job field Science and research Medical Faculty of Masaryk University, Brno, Czech Republic, invites excellent scientists to apply for Postdoc position in Bioinformatics in Stem Cell Neurobiology   Description: The Department of…

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About ‘Estimated Number of cells’ in snRNA-seq

About ‘Estimated Number of cells’ in snRNA-seq 0 Hi all, I am analyzing single nucleus RNA-seq data using Seurat. And I have total four group and 24 samples (Brain region A Control & case and Brain region B Control & case; each n=6). I wonder what is the appropriate range…

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Integrating Bulk RNA-seq data with Single cell RNA seq data

Integrating Bulk RNA-seq data with Single cell RNA seq data 0 Hello all, recently, I had been trying to integrate bulk RNAseq data into single-cell data where I treat each sample in my bulk RNAseq data as a single cell and integrate it into the single-cell data based on the…

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Is there a database of bioinformatics tools & databases?

All – Some years ago I was speaking to Sean Davis Re: the plethora of bioinformatics tools and databases. I commented to him that merely keeping up with what is available is difficult in the context of a full-time job, let alone mastering what you feel to be the best-in-class…

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NA values for mitochondrial gene percentage

NA values for mitochondrial gene percentage 0 I am running Seurat on publicly available dataset of ~400k cells. More than 80% of the cells are returned as NA when I use percentageFeatureSet(object, pattern = “^MT-“). How should I interpret these result? Does this mean the 80% of cells are of…

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Bioinformatics Scientist, Discovery Biology job with Surrozen

Surrozen is a biotechnology company focused on discovering and developing novel regenerative medicines that unlock the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway. Surrozen was founded by five leading-edge scientists: K. Christopher Garcia, Ph.D., Roel Nusse, Ph.D. and Calvin Kuo, M.D., Ph.D. from…

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How do I access inflection points in Seurat object?

How do I access inflection points in Seurat object? 0 I ran the following code below to calculate inflection points for the UMI counts for my single cell data using Seurat. seurat_obj <- CalculateBarcodeInflections(seurat_obj,barcode.column = “nCount_RNA”,group.column = “orig.ident”,threshold.low = NULL,threshold.high = NULL) I want to obtain the inflection points so…

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Correct usage of FindConservedMarkers() in Seurat

Correct usage of FindConservedMarkers() in Seurat 0 Dear all, I have a Seurat object of a certain cell type with a UMAP of 7 clusters. I also have information about the sample’s origin (primary tumor/metastatic) in my metadata. Looking at the UMAP I can clearly see that clusters 1 and…

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Post Doctoral Research Associate Bioinformatics job with Beth Israel Deaconess Medical Center/Harvard Medical School

The Hide Lab at Harvard Medical School and BIDMC seeks a bioinformatics/computational biology postdoctoral fellow for training. We focus on target discovery, and diagnostic and therapeutic applications for Alzheimer’s Disease. The position is under the direction of Dr. Winston Hide (Systems RNA medicine) and is available immediately. For a list of publications…

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seurat, subcluster and trajectory analysis (Monocle 3)

seurat, subcluster and trajectory analysis (Monocle 3) 1 Hi all, I am analyzing single cell RNA-seq data using Seurat and would like the follow up the analysis with cell trajectory analysis using Monocle3. So I tried several methods, but I am not sure how to do it. I want to…

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Ph.D. Bioinformatics Specialist (Long-Term Contract) – NIH/NIEHS

Job:Ph.D. Bioinformatics Specialist (Long-Term Contract) – NIH/NIEHS – Research Triangle Park, NC 0 Kelly Government Solutions is a strategic supplier and business partner to the federal government and its key suppliers. We are seeking an individual to work as a Ph.D. Bioinformatics Specialist at the National Institutes of Health in…

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Error “start too small” when running htseq-count on a sorted .bam file

Error “start too small” when running htseq-count on a sorted .bam file 0 Hello, This is my first time aligning scRNA-seq reads to a reference genome to analyze differential gene expression. I am using htseq-count to obtain count files for my different samples and I am receiving the following error:…

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Why do some genes are more prone to dropout effect in scRNA-seq?

Why do some genes are more prone to dropout effect in scRNA-seq? 0 Dear Community, scRNA-seq analysis has its own conventions. For example, CD56 is a canonical protein marker for the identification of Natural Killer (NK) cells. However, in scRNA-seq analysis, NCAM1 (gene for CD56) is not commonly used. Instead,…

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vanheeringen-lab/seq2science – Giters

Seq2science is the attempt of the van heeringen lab to generate a collection of generic pipelines/workflows which can be used by complete beginners to bioinformatics and experienced bioinformaticians alike. Please take a look at our docs for help with installation, how to run it, and best practices. Our supported workflows:…

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No cell names (colnames) names present in the input matrix

CreateSeuratObject: No cell names (colnames) names present in the input matrix 2 I did scRNA-seq using patient PBMC, 4 biological replicates. Each PBMC was tagged with 4 different types of hashtag oligos and subjected to multiplexing. Using fastq files, cellranger multi was performed and 4 matrices were generated. Using Seurat,…

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The Biostar Herald for Tuesday, November 23, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Mensur Dlakic, Istvan Albert, and was edited…

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Seurat FeaturePlot blend and order

Seurat FeaturePlot blend and order 0 I am wondering if its possible to apply order = TRUE and blend = TRUE at the same time in FeaturePlot, because for the blended umap the ordering is still default. Basically bring the yellow dots up top. Thanks. FeaturePlot(Data.Combined.c3, features = c(“Gene1”, “Gene2”),…

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How to Analyze Read Counts datasets and UMI-Counts datasets in scRNA-seq

How to Analyze Read Counts datasets and UMI-Counts datasets in scRNA-seq 0 Hello! I am analyzing datasets with some having UMI-counts matrices, but some being read-counts matrices (they were sequenced with technologies that do not incorporate UMIs). According to this paper (UMI-count modeling and differential expression analysis for single-cell RNA…

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Is there a way to distinguish doublets from phagocytes performing efferocytosis in scRNA-seq data?

Is there a way to distinguish doublets from phagocytes performing efferocytosis in scRNA-seq data? 0 Hello everyone! Here is an interesting conundrum. It has been reported that phagocytes may contain so-called “passenger” transcripts that originate from engulfed apoptotic cells, which not only obscures the transcriptional profile of a true phagocyte…

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Asc-Seurat: analytical single-cell Seurat-based web application | BMC Bioinformatics

To demonstrate Asc-Seurat’s functionalities, we analyzed the publicly available 10× Genomics’ 3k Peripheral Blood Mononuclear Cells (PBMC) dataset [26], showcasing the analysis of an individual sample. In addition, we used a second PBMC dataset to demonstrate the analysis integrating multiple samples in Asc-Seurat. The second PBMC dataset was generated by Hang…

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Gene regulatory Network analysis using SCRNA-seq

Gene regulatory Network analysis using SCRNA-seq 0 Hi All, I am new to the scRNA_seq data analysis. Recently I analyzed a treatment vs control scRNA-seq. Treatment group has samples treated with a compound, which has shown positive effect (reduction in disease). Purpose of the study is to understand the mechanism…

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integrated scRNA-seq dataset

integrated scRNA-seq dataset 0 I read a lot of methods about integration of multiple scRNA-seq datasets from different cohorts, species, or experimental designs. I’m curious about a question. It seems that almost all of studies try to explore “methodology” of integration rather than “application”. Is there any publications using one…

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Principal Component Analysis Rna Seq

Listing Results Principal component analysis rna seq Genomatix Principal Component Analysis For RNASeq Data Preview 2 hours agoThis is explained in detail on “RNA–Seq workflow: gene-level exploratory analysis and differential expression”. The matrix of raw counts is input to the DESeq2 rlog function and the resulting transformed matrix is used…

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Comparing gene expression between biological replicates

Spatial transcriptomics analyses: Comparing gene expression between biological replicates 0 Hi everyone, I have 10X Visium mouse brain data for 4 different conditions – 3 replicates per condition and two tissue sections per mouse. I am trying to understand the best way to approach gene expression analysis given this data;…

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How to quickly find and filter coexpressed markers with one specific gene of interest in individual cells using scRNA-seq data?

Hello Biostars Community, How to quickly and precisely, find and filter coexpressed markers with one specific gene of interest in scRNA-seq data? Is there a way to do this, without making a gene-gene correlation matrix (takes wayyy too long)… Using clustering often just groups together cells with similar expression patterns,…

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sequencing – Plotting QC output for scRNA data analysis using Seurat R and accessing Seurat object data

I am new to R, and want to analyse some public scRNA seq data published in Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP et al. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Cell 2018 Nov 1;175 (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120575). I have tried to follow the online…

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Seurat sctransform – does anyone know of a good explanation for biologists?

Seurat sctransform – does anyone know of a good explanation for biologists? 0 Hi, I was wondering whether anyone knows of a good blog/video/post explaining sctransform in a clear and easy to understand way. I understand the idea of the approach but would like to further understand the details. The…

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GEOquery with R

GEOquery with R 0 I am trying to start some analysis of RNA seq data with R. However, I am having some trouble with downloading the data. I have downloaded the following libraries: install.packages(“BiocManager”) install.packages(“forcats”) install.packages(“stringr”) install.packages(“ggplot2”) install.packages(“ggrepel”) install.packages(“readr”) install.packages(“tidyr”) install.packages(“survminer”) BiocManager::install(“GEOquery”) BiocManager::install(“limma”) BiocManager::install(“pheatmap”) BiocManager::install(“org.Hs.eg.db”) Ran this code: library(GEOquery) gse…

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Complexity of gene expression data in scRNAseq

2 hours ago esergison • 0 Hello, I’m a biologist trying to understand some scRNAseq data. I’ve been following this tutorial: github.com/hbctraining/scRNA-seq/blob/master/lessons/04_SC_quality_control.md I’m looking at dot plots of complexity that graph unique transcripts vs sequencing reads and I’m having trouble understanding what complexity means here. Is this a way of…

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some questions about sample, integration and subcluster

some questions about sample, integration and subcluster 0 Hi, every teacher, I’m new in scrna-seq and i had read some posts about scrna-seq, but there are several questions which make my confused: how to qualify a bad sample(not a cell),and should a bad sample be abandoned? i test 3 samples…

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Why only reverse fatsq file is used for mapping step in single cell RNA sequencing analysis?

Why only reverse fatsq file is used for mapping step in single cell RNA sequencing analysis? 1 Dear all, I am following a tutorial to do ScRNA-Seq analysis. In the mapping step it has been advised to use the reverse strand, however I don’t understand the logic behind this. Can…

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Review of popular science: analysis and comparison of single-cell RNA sequencing methods

Using 2i/LIF and ERCC inserted RNA cultured mouse embryonic stem cells (mESCs) as materials, using 6 different library preparation methods (CEL-seq2/C1, Drop-seq, MARS-seq, SCRB-seq, Smart-seq /C1 and Smart-seq2) prepare single-cell RNA-seq data. The difference between these methods lies in the use of unique molecular marker (UMI) sequences, which can distinguish…

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Researchers Submit Patent Application, “Immune Profiling Using Small Volume Blood Samples”, for Approval (USPTO 20210324447): Patent Application

2021 NOV 05 (NewsRx) — By a News Reporter-Staff News Editor at Insurance Daily News — From Washington, D.C., NewsRx journalists report that a patent application by the inventors Brown, David (Pasadena, CA, US); Dobreva, Tatyana (Pasadena, CA, US); Park, Jong Hwee (Pasadena, CA, US); Thomson, Matthew W. (Pasadena, CA,…

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analyzing spatial transcriptome data (Part 2)

Recognition of spatial variable features Seurat Two workflows are provided to identify molecular features related to tissue spatial location . The first is differential expression according to the pre labeled anatomical regions in the tissue , This differential expression can be determined by unsupervised clustering or a priori knowledge ….

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Advanced Bioinformatics Data Scientist job at BenevolentAI, November 2021

With over 35 nationalities and a range of backgrounds represented in our Benevolent team, we aim to build an inclusive environment where our people can bring their authentic selves to work, be respected for who they are and the exceptional work they do. We welcome and actively encourage applications from…

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Bioconductor – genomicInstability

DOI: 10.18129/B9.bioc.genomicInstability     Genomic Instability estimation for scRNA-Seq Bioconductor version: Release (3.14) This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of…

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Bioconductor – TENxPBMCData

DOI: 10.18129/B9.bioc.TENxPBMCData     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see TENxPBMCData. PBMC data from 10X Genomics Bioconductor version: 3.11 Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics. Author: Kasper D. Hansen [aut], Davide Risso [aut], Stephanie Hicks [aut,…

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BAMboozle removes genetic variation from human sequence data for open data sharing

Strategy for stripping human sequence data of genetic information To lower the barriers in sharing sequence data, we propose, like others recently17, to remove information on genetic variation that could be used to infer the identity from aligned reads and compromises the privacy of the donor (Fig. 1a). Genetic variation, including…

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How to split hashtag fastq?

How to split hashtag fastq? 0 We have hashtag scRNA-Seq data (fastq1, fastq2, HTO-fastq1, and HTO-fastq2) each including 6 samples. We know that there are ways to calculate counts for each UMI for each sample (scRNA-seq CITE-seq-count bioinformatics). However, we would like to split the fastq files by the sample….

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To merge technical sequencing replicates or not to merge?

scRNA-seq: To merge technical sequencing replicates or not to merge? 0 HI all, I have sorted single cells in 10 96well plates and performed SmartSeq2. A couple of the plates had to be resequenced as the desired depth of 1Mreads/cell was not reached for a few of them. I am…

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Why ‘junk DNA’ is critical for our survival

Nearly half of our DNA has been written off as junk, the discards of evolution: sidelined or broken genes, viruses that got stuck in our genome and were dismembered or silenced, none of it relevant to the human organism or human evolution. But research over the last decade has shown…

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Single-Cell RNA Sequencing May Be Split By Parse Biosciences

When Alex Rosenberg, PhD, and Charlie Roco, PhD, were graduate students in Georg Seelig’s lab at the University of Washington, they drew out their idea for how to increase the scalablility of single-cell RNA sequencing (scRNA-seq) on a whiteboard. At that time, roughly five years ago, “large scale was about…

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Finding cluster specific markers in the Seurat object

Finding cluster specific markers in the Seurat object 0 Hello I have a basic question, I have done found top marker in the Seurat object, however using Violin plot shows this marker are not specific for the clusters. I used average expression function but it couldn’t help me for this…

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Re-analysis of multiple scRNAseq data

Re-analysis of multiple scRNAseq data 1 Hi all, Is it possible to recombine several old scRNA seq studies and answer a biological question i.e. build up a new analysis on the basis of combine analysis of old. EXAMPLE -I found many single cell RNA seq studies which focus on different…

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Bioinformatics Scientist II – 64019 Jobs in Philadelphia, PA – Children’s Hospital of Philadelphia

Location: LOC_ROBERTS-Roberts Ctr Pediatric Research Req ID: 113752 Shift: Days Employment Status: Regular – Full Time Job Summary The Bioinformatics Unit (BIXU) within the Center for Data Driven Discovery (D3b) at The Children’s Hospital of Philadelphia (CHOP) is seeking a level II Bioinformatics Scientist to join our over 30 professional…

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Odd-looking cell cycle scores in scRNA-seq data

Odd-looking cell cycle scores in scRNA-seq data 0 I’ve performed the cell cycle scoring using the scanpy workflow. When I visualise the phase I get the following plot: It seems that some cells have a vastly differing profile from the rest. Because of this, I can’t really tell if the…

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How to identify the cell type computationally when you have a list of conserved cell type markers for mouse genome (as discovered by Seurat)?

How to identify the cell type computationally when you have a list of conserved cell type markers for mouse genome (as discovered by Seurat)? 0 I have a list of conserved cell type markers discovered from Seurat. I would like to annotate clusters with cell types based on that. For…

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KEGG passway analysis after Seurat analysis

KEGG passway analysis after Seurat analysis 0 Hello, everyone. I am so sorry for this amateur question. I have a scRNA-seq data and want to compare and visualize the expression levels across genes on a cluster by using clusterprofiler package (passway analysis), but I think the average expression levels of…

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Bioconductor – scDataviz

DOI: 10.18129/B9.bioc.scDataviz     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see scDataviz. scDataviz: single cell dataviz and downstream analyses Bioconductor version: 3.12 In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need…

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Editing Hash.ID in a Seurat Object

Editing Hash.ID in a Seurat Object 0 Hello, I integrated 12 samples that have following Seurats integration protocol here. These samples where each hashed based on their stimulation condition (two protein stimulations and one unstimulated). When I run DimPlot(Data_group1, reduction = “umap”, cols=pal, group.by = “hash.ID”) I get back a…

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Scientist II, Cancer Immunologic Data Commons

Scientist II, Cancer Immunologic Data Commons Dana-Farber Cancer Institute Boston, MA Full Time PTL Remote: 2-3 days remote/wk The Department of Data Science seeks a Scientist II to lead the development of the Cancer Immunologic Data Commons at Dana-Farber. The Scientist II will work closely with the laboratories of Drs.Franziska…

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If four groups (2 cell lines +/- treatments) of single cell RNA seq available, do I have to analyze each of the four datasets seperately?

If four groups (2 cell lines +/- treatments) of single cell RNA seq available, do I have to analyze each of the four datasets seperately? 0 I have our groups (2 cell lines +/- treatments) of single-cell RNA seq data. I used cellranger count and cellranger aggr to generated the…

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Different index than annotated genome scRNA-seq/troubleshooting : bioinformatics

Hi All, When pre-processing scRNA-seq data I have accidentally used different indexes (Hg19) for alignment in comparison to the gene annotation file I used for count quantification (GRCh38). I am using publically available data and my workflow seems to have achieved the same/better levels of alignment (~70%) than the original…

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Neuroscientists Roll Out First Comprehensive Atlas Of Brain Cells

When you clicked to read this story, a band of cells across the top of your brain sent signals down your spine and out to your hand to tell the muscles in your index finger to press down with just the right amount of pressure to activate your mouse or…

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So-Called Junk DNA Plays Critical Role in Mammalian Development

Nearly half of our DNA has been written off as junk, the discards of evolution: sidelined or broken genes, viruses that got stuck in our genome and were dismembered or silenced, none of it relevant to the human organism or human evolution. But research over the last decade has shown…

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Single cell RNA-seq analysis using a Galaxy interface

In this webinar, we will look at a Galaxy interface for single cell analysis. Specifically, we will run Scanpy (which would otherwise require Python programming skills) to analyse a Drop-seq dataset located in EMBL-EBI’s Single Cell Expression Atlas. Who is this course for? This webinar is aimed at individuals…

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use files with same name as input? : bioinformatics

Hi everyone, I have a question regarding the input of several fastq files into ‘CellRanger count’ pipeline.I performed scRNA-seq of different samples at a partner institute and the sequencing facility started by sequencing all the samples at a lower depth (to test the quality of the libraries) and only then…

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In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger?

In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger? 0 In single cell RNA-seq, do we perform regular quality checks and adapter trimming (just like in regular RNA-seq) before using cellranger? cellranger adapter_trimming QC scRNA-seq • 10 views • link 2 hours ago…

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GEO scRNA-seq entry with cell type information?

GEO scRNA-seq entry with cell type information? 1 Hello, I am trying to look for a scRNA-seq dataset hosted in GEO that, apart of the common files genes.tsv, barcodes.tsv and matrix.mtx, also has a file mapping barcode to cell types (as annotated by the paper). I have been trying to…

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How to perform sequence quality filtering of raw reads for single cell RNA seq?

How to perform sequence quality filtering of raw reads for single cell RNA seq? 0 I have a few single-cell RNA-seq samples (raw fastq reads). When I process raw reads, what should I do first? Is it demultiplexing? If so, what is the best tool I can use? Can I…

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use files with same name as input

Cell Ranger count pipeline: use files with same name as input 0 Hello, I have a question regarding the input of several fastq files into ‘CellRanger count’ pipeline. I performed scRNA-seq of different samples at a partner institute and the sequencing facility started by sequencing all the samples at a…

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Twice as many nFeature_RNA than nCount_RNA = more cell complexity? but how?

Twice as many nFeature_RNA than nCount_RNA = more cell complexity? but how? 0 Hi, I am re-analysing a publicly available single-cell RNA-seq dataset with two samples (plus minus treatment) and have downloaded preprocessed data from the geodataset as two .csv files. The authors state these files contain matrices that have…

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