Tag: scRNA

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)…

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)…

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…

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…

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,…

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…

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…

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…

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…

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…

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,…

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…

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…

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…

# 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…

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…

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…

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…

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…

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:…

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,…

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…

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…

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]…

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…

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…

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…

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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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…

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…

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…

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…

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…

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)…

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…

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…

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…

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…

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…

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:…

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…

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…

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…

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…

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…

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…

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,…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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)….

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…

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…

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…

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…

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…

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…

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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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…

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…

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…

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…

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)….

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…

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…

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…

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…

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:…

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…

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…

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…

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…

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…

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…

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…

gRNA mutations prevent gRNA detection We transformed A549 cells expressing a tamoxifen-inducible Cas9 with a lentiviral pool for expression of 120 gRNAs (Supplementary Table 1) at low multiplicity of infection. After stringent selection using puromycin and 2 days of Cas9 induction, cells were allowed to grow for another 5 days. Next,…

The onset of embryo-specific gene transcription, also known as embryonic genome activation (EGA), is a crucial step in the developmental journey of an organism. Although EGA has been studied to some extent in mice, human EGA remains largely unexplored, mainly due to the lack of novel in vitro cell models…

MED-ZSFG-EXPMFull Time74386BRJob SummaryThe Rutishauser Lab, in the UCSF Division of Experimental Medicine, at Zuckerberg San Francisco General Hospital, is hiring an experienced Bioinformatics programming professional with a broad understanding of computational algorithms and systems to work on projects that utilize single cell RNA/TCR sequencing, epigenetic profiling, and multi-omics approaches to…

Bioconductor – scater Single-Cell Analysis Toolkit for Gene Expression Data in R. Bioconductor version: Release (3.17) A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization. GitHub – jimhester/scater: Single cell analysis tools for… Feb 3, 2016 ·…

Forum:scRNAseq Differential expression analysis 0 Hello everyone! I am a student that recently started working with transcriptomics data. I am trying to conduct my first single cell data analysis of an organoid model using mainly Seurat. I tried to conduct a differential expression analysis between different clusters using the FindMarkers()…

Hi biostars, Ongoing improvements to multiple aspects of Oxford Nanopore (hereinafter, ONTTF) sequencing have led to substantive increases in single-base calling accuracy. Specifically, many of the most important advances have occurred since 2021 … Because this is changing so fast, I worry that even fairly recent, well-performed studies and methodologic…

News:Workshop – Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin) 0 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 Link? Website In…

Research Engineer Position in Bioinformatics at Institut Pasteur Paris – Research – Institut Pasteur” Postdoctoral Researcher in Computational Biology / Bioinformatician Engineer Post-Doctoral Researcher Position in phylogenomics and pangenomics Emploi Research Engineer Position in Bioinformatics at Institut Pasteur Paris Équipe: Hub de Bioinformatique et Biostatistique Équipe: Interactions cerveau-immunité Département de:…

Is it okay to just average the log2FC values across different cell types in pseudobulk scRNA-seq data? 0 Hi! I downloaded a differential gene expression summary data table like this from brainSCOPE. All I need is “gene” and “log2FoldChange” column. However, each gene’s data is split into multiple different cell…

Is there an easy to modify the subplot titles in DimPlot (Seurat)? 3 Dear experts, When using DimPlot to plot the UMAP for the combined Seurat object, say it includes two groups, the combined object after the Dimplot will become one patchwork gg ggplot structure, while how to change each…

DOI: 10.18129/B9.bioc.ROSeq   Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data Bioconductor version: Release (3.17) ROSeq – A rank based approach to modeling gene expression with filtered and normalized read count matrix. ROSeq takes filtered and normalized read matrix and cell-annotation/condition as input and determines the differentially…

Hello, I am doing deconvolution on bulkRNA data from mice brain. I would like to know the proportions of Oligodendrocytes, astrocyte, etc. According to Cibersortx tutorial 1, my first step is to build a signature matrix file from my own single-cell sequencing data. But I got an error saying ‘object…

Pre-processing for single cell RNAseq: Hard thresholds, data (cluster)-driven or both? 0 Prior to analyzing single cell RNAseq datasets, I typically employ a pipeline where I look at QC metrics, apply some hard filter, cluster the data, then re-examine the QC metrics, and update the hard filter. I’m now wondering…

Paired vs Unpaired t-test: Compositional analysis in the Human snRNA-seq data 0 Hi all, I have a 6 case and 6 age-, gender-matched control human brain snRNA-seq data (one-to-one matched). All samples were integrated and analyzed together, and I would like to compare the difference in cell proportion between control…

How to split grouping information in a single expression matrix? 1 Hello everyone, I am a rookie in single-cell RNA seq analysis. Currently, I am learning to analyze the data (GSE150703) in R. The colname is like NORM_P14_WR_Mccarrol_r3_CGGTAATTGCCC and OIR_P17_WR_Joyal_r1_TCGCGCCACTAG. When I read the table and created a Seuratobject I…

Is it okay to normalize data once more? 0 I am building deep learning classification model for scRNA, currently, but datas that I processed different normalization. My deep learning model use normalize_per_cell in scanpy, but some of datasets have raw expression count data, and some processed RPKM before. Is it…

A surprisingly low number of genes define the trained muscle To study differences between untrained and endurance-trained muscles (in the present study, muscle always refers to quadriceps), mice were exercised by treadmill running on 5 d per week for 1 h. After 4 weeks, a significant improvement in running performance was observed (Extended…