Tag: scRNA

Exploring the Latest Advances in Transcriptomics

Since the idea of genetic regulation was first postulated back in the 1950s, our scientific understanding of the transcriptome has deepened greatly.1 Looking into the transcriptome of cells and tissues has helped scientists to understand the biological processes that drive both health and disease; however, the complex and occasionally mysterious…

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My paired end data became single end data after mapping

My paired end data became single end data after mapping 1 Dear community, Something weird happened to me, my public dataset is obviously paired-end data (stated in ‘metadata’ part of ENA database, and there are two seperate fastq files (R1 & R2) and index file (I1) per sequencing run). After…

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The Biostar Herald for Tuesday, December 19, 2023

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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scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts?

scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts? 1 @03836aaf Last seen 5 hours ago United States Hi, I’m using AggregateExpression() function to convert my scRNA-seq data into pseudobulk for differential expression with Deseq2. I’m wondering whether AggregateExpression() simply sums the counts for each gene in each cell, or…

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Functional-metabolic coupling in distinct renal cell types coordinates organ-wide physiology and delays premature ageing

Preferential carbohydrate import and early metabolism in PCs (but not SCs) supports renal physiology independent of ATP production Drosophila renal (Malpighian, MpT) tubules consist of two major cell types, the larger PCs and smaller SCs which perform distinct roles in ion, solute and water transport (Fig. 1a, b)16. These functional differences…

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Metagenome analyses identify human endogenous retrovirus-K113 (HML-2) subtype in glioblastoma. Reply

. 2023 Dec 15;133(24):e176406. doi: 10.1172/JCI176406. Affiliations Expand Affiliations 1 Miller School of Medicine, Department of Neurological Surgery, University of Miami, Coral Gables, Florida, USA. 2 National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA. Item in Clipboard Vaidya Govindarajan et al. J Clin Invest. 2023. Show details Display…

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Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma

Whole-genome sequencing (WGS) analysis of early and advanced adenocarcinomas Whole-genome short read and long read sequencing datasets of 76 lung cancer specimens were analyzed. The datasets included newly generated data for 48 early small-sized lung adenocarcinoma cases (collectively called “Early-Ad” hereafter). These cases included 26 AIS (9 and 17 cases…

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Computational Biology, Bioinformatics Internship – Summer 2024 at Takeda Pharmaceutical

By clicking the “Apply” button, I understand that my employment application process with Takeda will commence and that the information I provide in my application will be processed in line with Takeda’sPrivacy Noticeand Terms of Use. I further attest that all information I submit in my employment application is true…

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Single-cell analysis of chromatin accessibility in the adult mouse brain

Tissue preparation and nucleus isolation All experimental procedures using live animals were approved by the SALK Institute Animal Care and Use Committee under protocol number 18-00006. Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56–63-day-old mice and sectioned into 600 µm coronal sections along the anterior–posterior…

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Single Cell Data Scientist at European Molecular Biology Laboratory (EMBL)

About the team/job We are looking for a Bioinformatician to join the Open Targets data team. We are seeking an enthusiastic team member to expand our informatics platforms through the integration of single cell omics data to enhance drug discovery. This role would suit someone with experience in data integration…

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Investigating the prognostic value of mTORC1 signaling in bladder cancer via bioinformatics evaluation

mTORC1 signaling in bladder cancer Initially, we assessed the mTORC1 signaling scores of both normal and bladder cancer samples. We analyzed the TCGA dataset and observed that the mTORC1 signaling score in normal tissues was considerably lower than that in breast cancer tissue samples (Fig. 2A). We analyzed the expression of…

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What does each point represent in a volcano plots for RNAseq data?

What are the advantages and disadvantages of RNA-seq compared to other methods for studying gene expression?5 answersRNA-seq has several advantages over other methods for studying gene expression. Firstly, RNA-seq can detect new transcripts and coding regions, which is not possible with microarray technology. Secondly, RNA-seq provides less noisy data compared…

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Working with infercnv results for large datasets

Working with infercnv results for large datasets 0 I’m currently working with infercnv on a large dataset of 10x scRNA. I want to meaningfully visualise the results but with the resulting matrix of cnv results being so large it becomes prohibitive to visualise even with rasterisation. I was wondering if…

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VSCode python terminal crashes after trying to train a PyTorch model

I’m using scanpy to train a scRNA model, however, whenever I pass my dataset (AnnData), it simply crashes the terminal: if train: sc_model = RNAStereoscope(sc_adata) sc_model.train(max_epochs=2) sc_model.history[“elbo_train”][10:].plot() sc_model.save(“scmodel”, overwrite=True) else: sc_model = RNAStereoscope.load( r”.\scmodel”, sc_adata, ) Has anyone had this issue before? It doesn’t even give a proper error, it…

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Postdoctoral Research Fellow, Computational Biology / Bioinformatics @ Visterra

Summary Visterra is seeking a highly talented, self-motivated and innovative Postdoctoral Research Fellow to join our Technology Platform team. The fellow will lead the conceptualization and implementation of advanced machine learning approaches to large single cell, spatial and multi-omic datasets. The role will involve developing creative approaches to leverage machine…

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Bioinformatics Software Engineer Consultant Job at ProCogia

ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…

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Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction

Abstract Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map…

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scRNA data analysis , how to compare pattern in multiple samples

Hello Everyone . I am new to single cell data . in this path G:\RNA\sc\scdata I have 3 files Sample5D_barcodes Sample5D_features Sample5D_matrix.mtx I want to see cell clusters and differentially expressed genes for this single cell sample. I am running this command in R install.packages(c(“Seurat”, “ggplot2”, “Matrix”, “dplyr”)) library(Seurat) library(ggplot2)…

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ScRNAseq analysis scran :: quickcluster Error

ScRNAseq analysis scran :: quickcluster Error 1 @d4a334e3 Last seen 15 hours ago Germany Hello! I am having an error while doing normalization for my scRNAseq data, I would appreciate the help of anyone who countered the same problem the error is during quickcluster command as follow: clust <- quickCluster(sce)…

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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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What key technical adaptation to standard bulk RNAseq methods has enabled transcriptome profiling at the single-cell level?

How can transfer learning be used to cluster single-cell RNA-seq data across species and batch?5 answersTransfer learning can be used to cluster single-cell RNA-seq data across species and batch. SATURN is a deep learning method that learns universal cell embeddings by encoding genes’ biological properties using protein language models. By…

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Study reveals how maternal diabetes affects birth defects at the single-cell level

In a recent study published in Nature Cardiovascular Research, researchers from California used multimodal single-cell analysis in mice to investigate the mechanisms by which maternal diabetes mellitus contributes to congenital abnormalities in the fetus. They found that during embryogenesis, maternal diabetes alters the epigenomic landscape in cardiac and craniofacial progenitors,…

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what should I do if I get a compromised sample of scRNA-seq data?

what should I do if I get a compromised sample of scRNA-seq data? 0 Hi everyone, Recently, I got my snRNA-seq data. But after aligned to reference genome using cellranger, I got a wired barcode rank plot. what should I do next to correct this data? Thanks in advance scRNA-seq…

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4 Fastq files for a single run generated by 10X

4 Fastq files for a single run generated by 10X 0 Hello, I have a question about the 10X generated Fastq files. As I know 10X platforms can generate up to 4 Fastq files as R1, R2, I1 and I2. I need to use Fastq files and align them with…

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mouse+human cells in 10x scRNA-seq

mouse+human cells in 10x scRNA-seq 1 Hi everyone, I’m analyzing 10x scRNA-seq data generated from xenografts (mouse + human tissues). I have the following workflow to label cells as either mouse or human: Align 10x scRNA-seq data to mouse+human combined genome using cellranger count. Use the file generated by cellranger…

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From TPM to raw counts

From TPM to raw counts 0 I am deconvoluting a bulk RNASeq experiment using scRNA to generate a signature of cell types using CIBERSORTX. The program asks you bulk data normalized, so I used TPM. The finction ‘high resolution’ returns normalized expressione (I presume) per cell type. To perform differential…

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What are the papers using single cell rnaseq to study meiosis?

What is single cell?5 answersSingle cell refers to the analysis of individual cells at a high-resolution level, allowing for a deeper understanding of cellular behavior and mechanisms. It overcomes the challenge of cellular heterogeneity and provides new methods for studying the relationship between individual cells and the body. Single cell…

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Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability

Szekanecz, Z. et al. Autoinflammation and autoimmunity across rheumatic and musculoskeletal diseases. Nat. Rev. Rheumatol. 17, 585–595 (2021). Article  CAS  PubMed  Google Scholar  Rosenblum, M. D., Remedios, K. A. & Abbas, A. K. Mechanisms of human autoimmunity. J. Clin. Invest. 125, 2228–2233 (2015). Article  PubMed  PubMed Central  Google Scholar  Wang,…

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ProCogia hiring Bioinformatics Software Engineer Consultant in Vancouver, British Columbia, Canada

ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…

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East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease

We conducted a three-stage genome-wide analysis of PUD and its subtypes. An overview of the workflow is provided in Fig. 1 and Supplementary Fig. 1. PUD cases in the east Asian populations were obtained by combining individuals with any of the two major PUD subtypes (DU and GU), which were…

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Consistent low number of cells and low fraction reads across the samples

scRNA-seq: Consistent low number of cells and low fraction reads across the samples 0 Hi, cell ranger count returned the following representative result for a sample. But, this is consistent for all the samples in a project. The number of cells detected ranges from 19 to 35, and the fraction…

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Bioconductor Code: distinct

# distinct: a method for differential analyses via hierarchical permutation tests <img src=”inst/extdata/distinct.png” width=”200″ align=”right”/> `distinct` is a statistical method to perform differential testing between two or more groups of distributions; differential testing is performed via non-parametric permutation tests on the cumulative distribution functions (cdfs) of each sample. `distinct` is…

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Harmony integration PC variance explained

Harmony integration PC variance explained 0 Hi guys, I ran harmony on my seurat obj and then elbow plot to select the number of PCs for downstream analysis. I found that a number of the earlier PCs explain less variance than the subsequent PCs I am not sure how this…

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Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset

Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset 0 Hello all, I have some feature matrixes from a bulk RNA seq analysis pipeline, and I want to perform bulk deconvolution to get relative single cell proportions. Some of the samples are from WT mice, while others are from…

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RNA Contamination Tool for Developing Cell Samples

RNA Contamination Tool for Developing Cell Samples 0 Hello everyone, I’m currently working on a project involving developing cell samples, and I’m encountering some challenges regarding RNA contamination. Most of the existing tools and assumptions regarding RNA contamination in single-cell RNA analysis seem to be based on adult tissue, where…

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Are liger or Seurat CCA good strategies for multiple scRNA-seq data integration?

Are liger or Seurat CCA good strategies for multiple scRNA-seq data integration? 1 Hi, I am working on analyzing multiple scRNA-seq dataset from embryonic tissues at progressive stages. I used three recent integration algorithms 1) liger, 2) Seurat CCA and 3) fastMNN. I started with these based on recommendation from…

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Online expert taught RNA-Seq workshop

News:Online expert taught RNA-Seq workshop 0 Edinburgh Genomics popular expert tutor taught online RNA-Seq courses are returning in December… Learn about bulk RNA-Seq and differential expression analysis 4-7th December RNA-Seq analysis register here Learn about scRNA-Seq analysis 11-12th December scRNA-Seq analysis register here workshop • 29 views Read more here:…

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Cataloging bacterial diversity within tumor samples

It is said in Spanish, “si no existe, créalo” or “if it does not exist, create it.” This is exactly what sometimes occurs at the Fred Hutch. When we do not have the tools to test a hypothesis, we must be creative! A great example is a collaboration between Dr. Susan Bullman,…

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The Biostar Herald for Monday, November 20, 2023

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 Istvan Albert, and was edited by Istvan…

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What are the advantages and disadvantages of bulk RNA and scRNA techniques?

How do environmental factors influence tumor development and progression? 5 answers What’s the importance of Epidrugs in breast cancer therapy? 3 answers Why are ion channels used as drug targets ? 3 answers How do genetic factors influence tumor development and progression? 5 answers Are herbal medicines effective chemopreventive agents…

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an extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input

error while running cellranger: an extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input 1 Hi, I’m quite new to scRNA-seq and I got an error as below while trying to run cellranger (version 7.2.0) for public human brain cortex data. [error]…

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Batch effect correction between Bulk RNA-Seq and scRNA-Seq’s clusters

Batch effect correction between Bulk RNA-Seq and scRNA-Seq’s clusters 1 Hello, I need to compare some samples from different bulk RNA-Seq with some clusters of a scRNA-Seq (not whole sample) to find DEGs. We have undifferentiated samples performed by bulk RNA-Seq and fully differentiated samples (mature ones) are 2-3 clusters…

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MAJOR Computational Biology Research Lab

MAJOR Computational Biology Research Lab (MCBRL) uses computer science algorithms to solve biology related problems, bioinformatics software development and develop bioinformatics cloud computing platforms or services for handling and analyzing large-scale biological data.. The workflow of hdWGCNA analysis for Single-cell Spatial Transcriptomics data RNA-seq Schematicsc/nRNA-seq Schematic ” RNA-seq Schematic 空间转录共表达网络分析流程…

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Deconvolution using cibersortx, help with real example

Hello Biostars, I have been stuck on an issue for quite some time now, and I hope someone can help me or point me in the right direction. I’ve received my bulk RNA fastq files and analyzed it in R using DESeq2. I have found an article that provide snRNA-seq…

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MD Anderson Cancer Center hiring Associate Bioinformatics Data Scientist in Houston, TX

SummaryThe University of Texas MD Anderson Cancer Center in Houston is one of the world’s most respected centers focused on cancer patient care, research, education and prevention. It was named the nation’s No. 1 hospital for cancer care in U.S. News & World Report’s 2022-2023 rankings. It is one of…

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Senior Bioinformatics Scientist @ Storm3

⚡ Senior Bioinformatics Scientist (HUMAN GENETICS) 🧪 Healthtech Start-Up 📌 Remote (US) 💰 $150K Base + Bonus + Impressive equity Are you interested in joining a revolutionary Biotech start-up that is using their ground-breaking AI platform to change the way we discover drugs? This established start-up with over $30M in…

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The Imageable Genome | Nature Communications

For the Imageable Genome project, we developed a data pipeline that identifies texts containing radiotracers, recognizes and extracts names of radiotracers from texts, filters for clinically relevant radiotracers and their associated targets, and translates protein names, i.e. of radiotracer targets, to names of the coding genes. We then downloaded the…

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scRNA-seq quality control

scRNA-seq quality control 0 Hi, Based on the literature, some genes like Gm42418, AY036118 and Malat1 are indicators of rRNA contamination or low quality cells and are suggested to be removed from the count matrix before normalization. I am dealing with a dataset that after removal of controversial genes (MT…

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Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens

Developing an epigenetic screening platform in human T cells Staphylococcus aureus Cas9 (SaCas9) has been extensively used for genome editing in vivo as its compact size (3,159 bp) relative to the conventional Streptococcus pyogenes Cas9 (SpCas9) enables packaging into adeno-associated virus26,27,28. However, SaCas9 has not been widely used for targeted gene…

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Single-cell dynamics of liver development in

image:  Integrated map of scRNA-seq and snRNA-seq data from pig livers at four time points and cellular heterogeneities within each major hepatic cell types. view more  Credit: ©Science China Press This study is led by Prof. Lusheng Huang (National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural…

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Postnatal Pig Liver Development Explored Through Single-Cell Dynamics

This study is led by Prof. Lusheng Huang (National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University). Liver executes essential metabolic and immunological functions throughout the postnatal periods, while cellular basis underlying postnatal liver development remains limited. Single cell technology facilitates the study of development at…

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How to solve error when annotating cell type with CellAssign

I want to use CellAssign to annotate scRNA-seq data, but I faced the error and I don’t know how to solve it. Could anyone help me? This is my code: rowdata <- rownames(N_data) coldata <- colnames(N_data) sce <- SingleCellExperiment(assays = list(counts = as.matrix(N_data)),colData = coldata,rowData = rowdata) sce <- computeSumFactors(sce)…

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convert matrix files from 10X (single cell) to h5 file

convert matrix files from 10X (single cell) to h5 file 0 For my single cell data, I have matrix files from 10X including (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for all my samples. I am trying to convert them to one h5 file per sample. to do so I used Create_10X_H5 function from…

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Visualize individual cell clusters colored by meta.data variable

Seurat: Visualize individual cell clusters colored by meta.data variable 0 Hello, I am analyzing a public scRNA dataset using Seurat. My goal is to observe variation inside individual cell clusters according to a condition (e.g. the diet) in a visual way using a dimensional reduction plot, e.g. observing sub-clusters of…

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Bioconductor – CDI

DOI: 10.18129/B9.bioc.CDI   Clustering Deviation Index (CDI) Bioconductor version: Release (3.18) Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be…

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Correct for different number of cells and individuals in single cell data analysis

Correct for different number of cells and individuals in single cell data analysis 0 I have scRNAseq from different donors for 4 different conditions. for different condition I have different number of donors and for different condition we have different number of cells. to make the conditions comparable, is there…

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Illuminating the Plant Gene Map

Climate change tests the resilience of farmers and their crops. To better understand how plants respond to their dynamic environments, scientists magnify the complex biological conversations between genes expressed in plant cells. Mapping out gene expression is informative, but traditional approaches for spatial understanding of gene expression are limited.  Tatsuya…

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CRISPR screening in hematology research: from bulk to single-cell level | Journal of Hematology & Oncology

Transcriptomics CROP-seq [46] Jurkat Poly-A CRISPRko Cas9 119 – 5798 (+ 1320 cells with NT gRNA) Lentiviral DROP-seq RNA Perturb-seq [43, 44] K562 Barcode CRISPRi dCas9-KRAB UPR epistasis screen: 9 triplet combinations UPR Perturb-seq experiment: 91 Up to 3 gRNAs in a single vector UPR epistasis screen: 15006 UPR Perturb-seq experiment:…

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Fasting-Mimicking Diet Drives Antitumor Immunity against Colorectal Cancer by Reducing IgA-Producing Cells | Cancer Research

Fasting-mimicking diet (FMD) is emerging as an effective dietary intervention with the potential to prolong life span in healthy people and boost antitumor immunity in patients with cancer. FMD refers to a medically designed fasting-like state that allows periodic consumption of a very-low-calorie and low-protein diet (1, 2). Compared with…

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When Glia Meet Induced Pluripotent Stem Cells (iPSCs)

Abstract The importance of glial cells, mainly astrocytes, oligodendrocytes, and microglia, in the central nervous system (CNS) has been increasingly appreciated. Recent advances have demonstrated the diversity of glial cells and their contribution to human CNS development, normal CNS functions, and disease progression. The uniqueness of human glial cells is…

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Postdoctoral Research Fellow, Computational Biology / Bioinformatics job with Visterra, Inc.

Summary Visterra is seeking a highly talented, self-motivated and innovative Postdoctoral Research Fellow to join our Technology Platform team. The fellow will lead the conceptualization and implementation of advanced machine learning approaches to large single cell, spatial and multi-omic datasets. The role will involve developing creative approaches to leverage machine…

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Unable to Generate Motif class for zebrafish scATAC data using Signac package.

Unable to Generate Motif class for zebrafish scATAC data using Signac package. 0 Hi, I am analyzing zebrafish scATAC data using Signac package. The package does not allow me to create motif class. It gives me the following error after running AddMotif function. `ATAC <- AddMotifs( object = ATAC, genome…

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Normalized data values very different from unnormalized counts in Seurat

Normalized data values very different from unnormalized counts in Seurat 0 I the sceasy R package to convert Burclaff et al.’s (2022) single-cell data (GSE185224) from scanpy H5AD data to a Seurat R object. My object’s UMAP looks similar to the authors, and I subsetted out “colon” samples. I then…

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Bioinformatic Scientist | Cleared Careers

Overview Axle is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations nationally and abroad. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques…

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Why I get different results from FindMarkers () while running the same script?

Why I get different results from FindMarkers () while running the same script? 0 Hi everyone, I am student that is approaching the omics field and I am running my first single-cell analysis in Seurat using a container. Recently, after a reboot of the server where my data is stored,…

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J. Craig Venter Institute hiring Bioinformatics Analyst (Zhang Lab) in La Jolla, CA

Position SummaryThe Zhang lab at the JCVI is looking for a highly motivated Bioinformatics Analyst. Projects will focus on integrative computational analysis of single cell multi-omics data, including single cell/nucleus RNA-seq data, using public and in-house experimental data assets. These projects will range across multiple organs and tissues to establish…

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MICA: a multi-omics method to predict gene regulatory networks in early human embryos

Introduction After the fusion of the oocyte and sperm, the zygote undergoes a series of cell divisions until it forms a blastocyst before implantation into the uterus. A human blastocyst is formed of a fluid-filled cavity and ∼200 cells that comprise three distinct cell types: the trophectoderm (TE), which gives…

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Bioconductor – GloScope (development version)

DOI: 10.18129/B9.bioc.GloScope   This is the development version of GloScope; to use it, please install the devel version of Bioconductor. Population-level Representation on scRNA-Seq data Bioconductor version: Development (3.18) This package aims at representing and summarizing the entire single-cell profile of a sample. It allows researchers to perform important bioinformatic…

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2-year Post-doctoral position in single cell genomics – Aarhus University – job portal

Department of Molecular Biology and Genetics – BiRC – Bioinformatics Research Center 2-year Post-doctoral position in single cell genomics Deadline 21 Nov 23:59 CET Expected start 1 Jan Department of Molecular Biology and Genetics – BiRC – Bioinformatics Research Center Universitetsbyen 81 8000 Aarhus C Fixed term full-time position 1…

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fragments file generation via Sinto from CellRanger output

fragments file generation via Sinto from CellRanger output 0 Hi, I am following the instructions for the PASTA package (satijalab.org/seurat/articles/pasta_vignette.html). This package uses scRNA-seq data to infer alternative polyadenylation usage from scRNAseq data. It requires among many input files also a fragment file. The authors state the following must be…

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Different “Reads Mapped Confidently to Transcriptome” values in scRNA

Hello everyone. My question is about sing-cell RNASeq. I am re-analyzing a scRNA raw data in my lab, which has previously analyzed by seqencing company, i am trying to replicate the results and update/optimize my pipeline. Currently my pipeline is as follows: 1. Creating custom reference I indexed the reference…

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A spatial sequencing atlas of age-induced changes in the lung during influenza infection

Single-cell RNA sequencing reveals cellular heterogeneity among young and aged lungs post-influenza infection In order to investigate age-induced alterations in the host response to influenza A virus (IAV) infection, we infected groups of three young (16–18-week-old) and three aged (80–82-week-old) female C57Bl/6 mice intranasally with 50 PFU of the PR8…

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Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages

Total Sdic mRNA abundance positively correlates with Sdic copy number in testis Evidence for the presumed enhancing effect of gene duplication on the amount of gene product is mixed. Some studies indicated that no such, or a very limited, effect exists19,38,39,40,41, whereas others found a significant increase17,18,22,42,43. A possible explanation…

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GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership | Genome Biology

Models for single-cell ATAC-seq data In single-cell ATAC-seq data, \(x_{ij}\) is the number of unique reads mapping to peak or region j in cell i. Although \(x_{ij}\) can take non-negative integer values, it is common to “binarize” the accessibility data (e.g., [19, 74, 133,134,135]), meaning that \(x_{ij} = 1\) when…

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Clustering resolution single-cell RNA-seq

Clustering resolution single-cell RNA-seq 1 Hi, I have a question about how to decide on the clustering resolution to use for single-cell RNA-sequencing datasets that contain multiple activation states rather than discrete cell populations. I have 10x Genomics scRNA-seq data from TCR-activated memory T cells from three donors (~2000-3000 cells/donor)….

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Bioinformatics software for single cell omics

Forum:Bioinformatics software for single cell omics 0 My professor asked me to find a software solution to deal with scRNA data analyses (preprocessing and analyzing data). The department is going to have VIZGEN and COSMX machine coming next quarter. 3-4 labs depend on 1 bioinformatician guy is really annoying and…

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r – Complication with clustree image generation

Running the below code (initially without par (lwd = 1) line ) returned the following error, and the same error was returned again after setting par(lwd = 1) or to 0.5 or 10. Truthfully don’t totally understand what’s going on when i change that variable other than that id be…

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MUSC College of Health Professions hiring UNIV – Research Specialist III- Bioinformatician – Department of Neuroscience in Charleston, South Carolina, United States

Job Description SummaryThe brand-new MUSC Bioinformatics Core (BioCM) is seeking a superb bioinformatician to develop scientific tools for single cell multiomics and other next-generation sequencing methods. Under the supervision and guidance of BioCM staff and Dr. Stefano Berto, the bioinformatician will contribute to NGS analysis projects, and they will work…

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GEO Dataset: Difficulty Understanding Matrices, Compliation

GEO Dataset: Difficulty Understanding Matrices, Compliation 1 Hi, I am new to using GEO, novice at R (have used seurat for my own scRNA data), apologies for how basic this question is: I am trying to replicate figure 1 from a recent paper using seurat. They’ve deposited their data as…

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FINAL CALL – Workshop – Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin)

News:FINAL CALL – Workshop – Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin) 1 Single-Cell RNA-Seq Data Analysis: A Practical Introduction Master the tools and techniques to confidently analyze single-cell RNA-seq data and gain new insights into complex biological systems When? November 8-10, 2023 Where? Berlin…

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Bioinformatics Analyst – NYU Langone Medical Center

NYU Grossman School of Medicine is one of the nation’s top-ranked medical schools. For 175 years, NYU Grossman School of Medicine has trained thousands of physicians and scientists who have helped to shape the course of medical history and enrich the lives of countless people. An integral part of NYU…

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Steps after doublet detection in single cell data

Forum:Steps after doublet detection in single cell data 0 Hello, I was wondering how everyone here deals with doublets. I used DoubletFinder on already clustered single cell data. DoubletFinder predicted that there are about ~8% doublets, and about 50% of them are part of 2 tiny clusters and another 50%…

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Storm3 hiring Senior Bioinformatics Scientist in United States

⚡ Senior Bioinformatics Scientist (HUMAN GENETICS) 🧪 Healthtech Start-Up 📌 Remote (US) 💰 $150K Base + Bonus + Impressive equity Are you interested in joining a revolutionary Biotech start-up that is using their ground-breaking AI platform to change the way we discover drugs? This established start-up with over $30M in…

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Researchers explore immunomodulating targets for improving glioblastoma therapies

In a recent article published in EMBO Molecular Medicine, researchers investigated cellular, molecular, and spatiotemporal heterogeneity of glioblastoma (GBM), a malignant and highly aggressive primary brain tumor. Study: Single-cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma. Image Credit: Triff/Shutterstock.com They performed single-cell ribonucleic acid sequencing (scRNA-seq) of…

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ROLE OF CATECHOLAMINERGIC A2 NEURONS OF NUCLEUS OF THE SOLITARY TRACT (NTS) IN CARDIOVASCULAR AND RESPIRATORY ADAPTATIONS TO CHRONIC INTERMITTENT HYPOXIA (CIH) IN RATS

Purpose: To understand the effect of CIH on the mRNA expression levels of AT1a, AT1b and excitatory amino acid (EAAs) receptor subunits in the A2 neurons of NTS and to assess the effect of tyrosine hydroxylase (TH) knockdown in A2 neurons on the cardiovascular responses to CIH Methods: Adult male…

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LAST CALL – Workshop – Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin)

News:LAST CALL – Workshop – Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin) 1 Single-Cell RNA-Seq Data Analysis: A Practical Introduction Master the tools and techniques to confidently analyze single-cell RNA-seq data and gain new insights into complex biological systems When? November 8-10, 2023 Where? Berlin…

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US Tech Solutions hiring Bioinformatics Scientist in United States

Title: Bioinformatics Scientist Job type: Contract Duration: 06+ Months Client’s Location: Remote Job Description: We are seeking a highly skilled and motivated contractor to join the Genomics Research Center and provide support for bioinformatics projects in the field of Ophthalmology and Specialty Medicine. As a contractor, you will collaborate with…

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A versatile regulatory toolkit of arabinose-inducible artificial transcription factors for Enterobacteriaceae

Design of arabinose-inducible artificial transcription factors A core objective of our work was to develop inducible, heterologous regulators capable of genetically reprogramming gene regulatory networks in Enterobacteriaceae, specifically Salmonella and E. coli. To achieve this, we designed arabinose-inducible ATFs incorporating diverse DBDs originating from CRISPR/dCas9 and plant heterologous TFs (Fig. 1)….

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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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Is APAC Edging Closer to Clinical Application of Single-cell Tech?

Asia Pacific (APAC) is expected to be a major contributor to the growth of single cell technology as the market is driven by factors such as the growing demand for personalised medicine, advancements in sequencing technologies, and the increasing use of single cell analysis in drug discovery. While Japan is…

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Transfer harmony-integrated scRNA-seq data to scanpy

Transfer harmony-integrated scRNA-seq data to scanpy 1 I have integrated two scRNA-seq datasets using harmony method. Unlike Seurat integration, Harmony just adds extra embeddings for further clustering and other analysis. However, the data (raw counts, normalized, and scaled slots) is the same as in unintegrated data. So, when I transfer…

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CITE-seq reveals inhibition of NF-kB pathway in B cells from vitamin D-treated multiple sclerosis patients

Abstract Vitamin D deficiency is a recognized risk factor for multiple sclerosis (MS) and has been associated with disease activity and progression. Vitamin D treatment has emerged as potentially protective, despite conflicting results from randomized controlled trials. Here, we used single-cell RNA-sequencing (scRNA-seq) combined with barcoded antibodies targeting surface markers…

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Subclustering of intergated cells from scRNA-seq data

Subclustering of intergated cells from scRNA-seq data 1 I used SCTnormalization and Seurat integration to integrate 3 scRNA-seq datasets. After manual annotation using RNA assay, I have one particular cluster of cells with overexpressed different T cells markers. So, to find heterogeneity of T cells I subclustered that particular cluster:…

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Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas | Acta Neuropathologica Communications

Single-nuclei RNA-sequencing analysis of NF1-associated plexiform neurofibroma reveals specific non-neoplastic and neoplastic cellular subpopulations Single-nuclei RNA-sequencing (snRNA-seq) was performed on 8 bulk frozen PN patient samples capturing approximately 4,000 nuclei per sample, a sufficient number of nuclei to provide adequate coverage to report the high levels of cellular heterogeneity found…

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Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas

doi: 10.1186/s40478-023-01639-1. Vladimir Amani  1   2 , Kent A Riemondy  3 , Rui Fu  4 , Andrea M Griesinger  5   6 , Enrique Grimaldo  5   6 , Graziella Ribeiro De Sousa  5   6 , Ahmed Gilani  7 , Molly Hemenway  6 , Nicholas K Foreman  5   6 , Andrew M Donson #  5   6…

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Chan Zuckerberg Life Sciences Computing System, Microsoft and Paige AI Partnership, Rehm Takes Chair of GA4GH

September 28, 2023 | Paige and Microsoft aim to build the world’s largest image-based AI models for digital pathology and oncology; Flatiron Health and FDA partner; HHS extends partnership with Regeneron; the GA4GH Board of Directors has elected Heidi Rehm to succeed Ewan Birney; and more.  Paige has joined forces…

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Allen Institute for Immunology hiring Manager, Bioinformatics Operations – Immunology in Seattle, WA

The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact…

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Bioconductor – mitch

DOI: 10.18129/B9.bioc.mitch   Multi-Contrast Gene Set Enrichment Analysis Bioconductor version: Release (3.17) mitch is an R package for multi-contrast enrichment analysis. At it’s heart, it uses a rank-MANOVA based statistical approach to detect sets of genes that exhibit enrichment in the multidimensional space as compared to the background. The rank-MANOVA…

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Enrichment of mitochondrial and ribosomal pathways

Enrichment of mitochondrial and ribosomal pathways – an artifact? 0 Hey everyone, In the last couple of years I’ve analyzed several different scRNA-seq of epithelial, and in most of these I found that one of the two groups of each experiment (different conditions each time) had enrichment of mitochondrial and…

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Abnormal developmental trajectory and vulnerability to cardiac arrhythmias in tetralogy of Fallot with DiGeorge syndrome

Generation and characterisation of patient-specific hiPSCs and hiPSC-CMs hiPSC lines were established from two TOF-DG patients, two TOF-ND patients, and two healthy controls with pluripotency markers and germ layer markers verified (Supplementary Figs. 1 and 2). Whole genome sequencing confirmed, respectively, the presence and the absence of 22q11.2 deletion in the…

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