Tag: scRNA

Bioconductor – EasyCellType

DOI: 10.18129/B9.bioc.EasyCellType     Annotate cell types for scRNA-seq data Bioconductor version: Release (3.16) We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA)…

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scRNA-seq for Microcephaly Research [I]: Single-Cell Droplet Encapsulation, mRNA Capture, and cDNA Synthesis

doi: 10.1007/978-1-0716-2752-5_8. Affiliations Expand Affiliations 1 Department of Medicine, Division of Immunology, Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, GA, USA. ben.babcock@emory.edu. 2 Department of Neurology, University of North Carolina Medical School, Chapel Hill, NC, USA. Item in Clipboard Benjamin Babcock et al. Methods Mol Biol. 2023….

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Bioinformatics Analyst II Job in Maryland (MD), Research and Development Career, Full Time Jobs in Frederick National Laboratory for Cancer Research

Bioinformatics Analyst II Job ID: req3154Employee Type: exempt full-timeDivision: Applied & Development Research ProgramFacility: Frederick: Ft DetrickLocation: PO Box B, Frederick, MD 21702 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical…

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Bioinformatics Scientist Job – Karkidi

Experience 2-4 year Salary $170,000-$180,000 Location San Francisco, CA, USA Job Function Bioinformatics Scientist Industry Information Technology Qualification Degree in Computer Science, PhD Degree, Degree in Bioinformatics, Degree in Computational Biology, Degree in Computational Science, Degree in Biomedical Engineering Key Skills Bioconductor, CRISPR technology, Data science techniques, Large data sets,…

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Pseudo-bulk DEG analysis with Multi-tissue in scRNA-seq

Hi all, I have 4 datasets (Brain region A (Control & Disease), Brain region B (Control & Disease)) and performed scRNA-seq by integrating all data. And I want to compare Disease and Control in each brain region using pseudo-bulk DEG analysis. (ex. Region A Disease vs Region A Control) Even…

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Is dropout a big concern (or factor) when analysing single cell RNAseq?

Is dropout a big concern (or factor) when analysing single cell RNAseq? 0 When analysing single cell RNAseq is drop-out (% dropout by count) a huge factor that needs to be paid attention? I see mixed opinions (publications, workshops, etc) on how to deal with dropouts whether to use imputation…

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Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline

Software Figure preparation: CorelDRAW x8 (Corel); Bioinformatic analyses: R v 4.0.3 (R Foundation for Statistical Computing). Computational resources Analyses were run on a desktop computer with an Intel Core i9-10900L CPU (3.70 GHz, 10 cores, 20 threads) with 120 GB RAM running Windows 10 Pro (v21H2). Data preprocessing scRNA-seq data sets…

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Single-cell Transcriptomics – SIB Training

Single-cell RNA sequencing (scRNAseq) allows researchers to study gene expression at the single cell level. For example, scRNAseq can help to identify expression patterns that differ between conditions within a cell-type. To generate and analyze scRNAseq data, several methods are available, all with their strengths and weaknesses depending on the…

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sr bioinformatics job | United States

linkedin.com Apply on Website The British Dental Journal Bioinformatics Research Scientist to develop and apply innovative analytical approaches to study the mechanisms of normal hematopoiesis and blood diso… Role: Research Scientist, Category: Scientific, Size: 1-10 Sr Bioinformatics Research Scientist: The British Dental Journal Bioinformatics Research Scientist to develop and apply…

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python – Correct way of merging scRNAseq datasets of healthy and tumor cell?

python – Correct way of merging scRNAseq datasets of healthy and tumor cell? – Bioinformatics Stack Exchange Stack Exchange Network Stack Exchange network consists of 182 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. Visit Stack…

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Opposing roles of hepatic stellate cell subpopulations in hepatocarcinogenesis

Villanueva, A. Hepatocellular carcinoma. N. Engl. J. Med. 380, 1450–1462 (2019). CAS  PubMed  Article  Google Scholar  Affo, S., Yu, L. X. & Schwabe, R. F. The role of cancer-associated fibroblasts and fibrosis in liver cancer. Annu. Rev. Pathol. 12, 153–186 (2017). CAS  PubMed  Article  Google Scholar  Mederacke, I. et al….

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Peripheral Neuroblastic Tumor Transcriptomes Point to Transitional Cell State

NEW YORK – With the help of single-cell RNA sequencing, investigators in China and Australia have untangled diverse tumor and microenvironment features for peripheral neuroblastic tumors (PNT), including a transitional tumor cell state that appears to coincide with more aggressive and difficult-to-treat forms of the pediatric neural crest cancers. “Historically,…

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How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger)

How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger) 0 Hello all. I am trying to pre-process some single cell RNA and ADT (Totalseq-C) data from an GEO SRA, but having some issues getting separate fastq’s for the “CITE-seq” (ADT)…

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Challenges of single-cell and single-nucleus RNA-sequencing from core needle biopsy specimens

Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) allow transcriptomic profiling of thousands of cells from a renal biopsy specimen at a single-cell resolution. Both methods are promising tools to unravel the underlying pathophysiology of glomerular diseases. KU Leuven researchers provide an overview of the technical challenges that should be…

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Subtype and cell type specific expression of lncRNAs provide insight into breast cancer

lncRNA expression according to breast cancer clinicopathological subtypes To identify lncRNAs expressed by specific breast cancer subtypes or associated with clinicopathological features, we analyzed RNA-sequencing data from two large independent breast cancer cohorts: SCAN-B (n = 3455)17 and TCGA-BRCA (n = 1095). We focused on lncRNAs annotated in the Ensembl18 v93 non-coding reference transcriptome…

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Bioinformatics Analyst in Minneapolis, MN for University of Minnesota, Twin Cities

Details Posted: 13-Aug-22 Location: Minneapolis, Minnesota Salary: 43944.32 – 123022.07 Categories: Research Support – Laboratory/Non-Laboratory Staff/Administrative Additional Information: 2 openings available. The Research Informatics Solutions (RIS) group within the University of Minnesota Supercomputing Institute (MSI) is hiring two full-time Bioinformatics Analysts to support research at the University of Minnesota. Analysts…

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Bioinformatics Analyst I – Job posted on UniversityJobs.com

We are looking for a Bioinformatics Analyst I. The position will involve analysis and visualization of large throughput multi-omics molecular profiles in various human disease models. Data types include single cell transcriptomics, proteomics, metabolomics and epigenomics analysis (MS proteomics and phosphoproteomics, scRNA-Seq, scATAC-Seq, scWGBS-Seq, scCut&Tag), and bulk tissue datasets spanning…

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Alternatives and detailed information of monocle3

Licence: other No description or website provided. Projects that are alternatives of or similar to monocle3 dropEst Pipeline for initial analysis of droplet-based single-cell RNA-seq data Stars: ✭ 71 (-58.24%) Mutual labels:  single-cell-rna-seq StackedDAE Stacked Denoising AutoEncoder based on TensorFlow Stars: ✭ 23 (-86.47%) Mutual labels:  single-cell-rna-seq kmer-homology-paper Manuscript for functional prediction…

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2 PhD candidates in Bioinformatics Stem Cells-Based Therapies Development

The Faculty of Science and the Leiden Academic Centre for Drug Research are looking for a:  2 PhD candidates in Bioinformatics Stem Cells-Based Therapies DevelopmentVacancy number: 22-435 Key responsibilities The research group of Prof. M. Drukker focuses on stem cell based therapeutics, and novel models for human disease and drug development….

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Senior Scientist Applied Bioinformatics Job In San Francisco, CA 94103| TechCareers

At Bristol Myers Squibb, we are inspired by a single vision – transforming patients’ lives through science. In oncology, hematology, immunology and cardiovascular disease – and one of the most diverse and promising pipelines in the industry – each of our passionate colleagues contribute to innovations that drive meaningful change….

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is scRNA-seq simply better than RNA-seq? : bioinformatics

Sorry if I am completely wrong and ignorant, I just started learning about RNA-seq since I may have to arrange protocols and experiments of RNA sequencing in the future. From what I read, scRNA-seq is an improvement over the bulk analysis of RNA-seq since it sorts the samples by its…

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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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