Tag: scRNAseq

Turncoat T cells are at the core of multiple sclerosis and other inflammatory central nervous system disorders

scRNAseq replicates. CD45.1+ P14 cells were adoptively transferred into adult CD45.2+ GP or GFAP:GP mice 24h before i.c. infection with rLCMV-GP33. At least six weeks later, mice were treated with antiCD8a depleting antibody or isotype control. One week after depletion, mice were treated with TAM i.p. for four consecutive days…

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Joint scRNAseq of B and T cells

Start Current SNIC Small Storage Projects SNIC 2022/23-318 Joint scRNAseq of B and T cells SUPR uses JavaScript for certain functions. We cannot guarantee that you will be able to use the system with JavaScript disabled. Primary Classification: 10605: Immunology (medical to be 30110 and agricultural to be 40302) Allocation…

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Best Pipeline for De novo transcriptome SC-RNAseq

Best Pipeline for De novo transcriptome SC-RNAseq 0 Hi everyone, I’m curious what the best pipeline for single cell RNA seq is if your organism of interest doesn’t have a genome. Tools such as CellRanger need a reference genome, and bustools seems to need a reference for indexing. Is the…

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Weird over-represented sequence in sn/scRNASeq fastqc

Weird over-represented sequence in sn/scRNASeq fastqc 0 Dear Fellows I have a a weird over-represented sequences in my sn/scRNASe samples founs in fastqc report as in the photo attached. I doubt that these sequences are the source of getting ambient RNA warning? Any idea how to remove them? thank you…

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Jobs on jobactive hiring Postdoctoral Bioinformatician in Single Cell and Spatial Omics Data Analysis in Adelaide, South Australia, Australia

Full-Time, 2 Year Contract Salary range $95,000 – $110,000 At the South Australian Health and Medical Research Institute (SAHMRI), we are committed to achieving innovative, ground-breaking health and medical research that fundamentally improves the quality of life for all people. The South Australian Genomics Centre (SAGC) is a multi-institutional, national…

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I don’t understand the HDF5 file from 10x genomics scRNAseq

I don’t understand the HDF5 file from 10x genomics scRNAseq 1 Hi! I have recently started my Phd and I’m trying to open a hdf5 file in R. He file is generated from 10x genomics cell ranger pipeline. Can someone please explain what i, P, Dim, Dimnames,x and factors means…

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Accepted r-bioc-scrnaseq 2.10.0+ds-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 17 May 2022 07:49:00 +0200 Source: r-bioc-scrnaseq Architecture: source Version: 2.10.0+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-scrnaseq (2.10.0+ds-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version:…

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scRNAseq analysis – h5ad file conversion to Seurat format

scRNAseq analysis – h5ad file conversion to Seurat format 0 Hi all. I have a single .h5ad file that contains scRNAseq data from several samples. I would like to convert it so that I can open it in Seurat (I am comfortable with R, but not with Python). I have…

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Glioblastoma scRNAseq Shows Treatment-induced, Immune-dependent Rise In Mesenchymal Cancer Cells, and Structural Variants in Distal Neural Stem Cells

This article was originally published here Neuro Oncol. 2022 Apr 13:noac085. doi: 10.1093/neuonc/noac085. Online ahead of print. ABSTRACT BACKGROUND: Glioblastoma is a treatment-resistant brain cancer. Its hierarchical cellular nature and its tumour microenvironment (TME) before, during, and after treatments remain unresolved. METHODS: Here, we used single-cell RNA-sequencing to analyze new…

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Sample management for enabling successful single-cell RNAseq processing

Analysis of single cells by sequencing (scRNAseq) provides insight into the impact of cellular heterogeneity on biological mechanisms and proper sample management is a critical aspect of large-scale clinical research studies, directly influencing downstream sample quality and the subsequent ability to interrogate specific cell populations of interest. Download this poster…

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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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3 arguments passed to .Internal(is.unsorted) which requires 2 #95

Kevinrue I am getting this error, using R 4.2.0 and Bioconductor 3.15: library(scRNAseq) > sce <- HermannSpermatogenesisData() […] Error in ..Internal(is.unsorted(x, FALSE, FALSE)) : 3 arguments passed to .Internal(is.unsorted) which requires 2 I’ve chased the issue down to this line (and the next) github.com/Bioconductor/S4Vectors/blob/338534bfb5fb6ada3f2abc144017bc8ce0aab6c3/R/isSorted.R#L149 That’s as far as I managed…

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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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Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

. 2022 Mar 3;220(3):iyac017. doi: 10.1093/genetics/iyac017. Affiliations Expand Affiliations 1 Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA. 2 Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403, USA. Item in Clipboard Hope M Healey et al. Genetics. 2022. Show details Display options Display options…

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secDrug: a pipeline to discover novel drug combinations to kill drug-resistant multiple myeloma cells using a greedy set cover algorithm and single-cell multi-omics

This article was originally published here Blood Cancer J. 2022 Mar 9;12(3):39. doi: 10.1038/s41408-022-00636-2. ABSTRACT Multiple myeloma, the second-most common hematopoietic malignancy in the United States, still remains an incurable disease with dose-limiting toxicities and resistance to primary drugs like proteasome inhibitors (PIs) and Immunomodulatory drugs (IMiDs).We have created a…

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Core-Bioinformatics/Lawrence-et-al-2021-scRNAseq: Code for single-cell RNA-seq processing and analysis for Lawrence et al. 2021

GitHub – Core-Bioinformatics/Lawrence-et-al-2021-scRNAseq: Code for single-cell RNA-seq processing and analysis for Lawrence et al. 2021 This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab…

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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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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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Bioinformatician in Biology, Physics, Mathematics – scRNAseq datasets – Gothenburg, Sweden

Department of Internal Medicine and Clinical Nutrition, at the Institute of Medicine invites applications for a bioinformatician interested in analysis of large single cell RNA sequencing (scRNAseq) datasets, at University of Gothenburg, Sweden – 2022 ADVERTISEMENTScroll Down for Content General Info Position: BioinformaticianNo. of Positions: 1 Research Field: Bioinformatics, Biology,…

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Cell type identification in scRNAseq

Cell type identification in scRNAseq 1 Hello all, I am working with the healthy data set [PRJNA562645]. I have used cell ranger pipeline to create count file and created seurat object and added the metadata info. but, I am really confuse about how to identify cell type. Can some one…

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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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Novel diagnostic biomarkers for keloid based on GEO database

Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…

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Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs

doi: 10.1093/nar/gkac019. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA. 2 Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA. 3 Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824, USA….

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Combining multiple 10x scRNAseq datasets

Hi everyone, Wondering if someone can provide me with some guidance. I have previously sequenced 4 skin cancers using 10X chemistries and I would like to combine them into one dataset. My research question is to look at cancer stem cell populations, so I will need sensitivity. I have done…

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SCHNAPPs – Single Cell sHiNy APPlication(s)

Abstract : Single-cell RNA-sequencing (scRNAseq) experiments are becoming a standard tool for bench-scientists to explore the cellular diversity present in all tissues. Data produced by scRNAseq is technically complex and requires analytical workflows that are an active field of bioinformatics research, whereas a wealth of biological background knowledge is needed…

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Single cell RNAseq data analysis

Github repository  02-04 February 2022  SciLifeLab Solna, Tomtebodavägen 23b, Stockholm, Sweden This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of online lectures and computer practicals. The total course duration is 45 hours, including the online lectures (15 hours)…

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STARsolo –EmptyDrops_CR parameters

STARsolo –EmptyDrops_CR parameters 1 I’m having some issues with the alignment of 10x scRNAseq data to a custom genome and I thought it would be good to do a stricter filtering on the cells so more cells get filtered out as empty droplets. Apparently STARsolo has several filtering algorithms, of…

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AbbVie hiring Senior Scientist I/II, Machine Learning Bioinformatics – (REMOTE Optional) in Cambridge, Massachusetts, United States

About AbbVieAbbVie’s mission is to discover and deliver innovative medicines that solve serious health issues today and address the medical challenges of tomorrow. We strive to have a remarkable impact on people’s lives across several key therapeutic areas: immunology, oncology, neuroscience, eye care, virology, women’s health and gastroenterology, in addition…

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Lee Placito Fellowship in Bioinformatics

Job Details Lee Placito Fellowship in Bioinformatics Nuffield Department of Surgical Sciences, Old Road Campus Research Building, Headington, Oxford Grade 7: £33,309 – £40,927 per annum Contract type: Fixed term for 3 years Hours: Full-time About the role We are looking for an enthusiastic bioinformatician who has an interest in…

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How to use “SingleR” on the marker genes from `FindAllMarkers` for each cluster?

How to use “SingleR” on the marker genes from `FindAllMarkers` for each cluster? 0 Hi, I tried to use SingleR to identify cell types for clusters. I have the table of results from FindAllMakers of Seurat package. I know that I can use: SingleR(GetAssayData(seurat.object, assay = assay, slot = “data”),…

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Poly A vs total RNA

Poly A vs total RNA – Which is better for extracting noncoding RNA information 0 Hi everyone, In scRNAseq ,I want to extract lncRNA,miRNA etc Extracted molecule -polyA RNA or total RNA Since polyA RNA will not give much information about noncoding counterpart,will it be fruitful to go on with…

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Looking for scRNAseq analysis tutor

Job:Looking for scRNAseq analysis tutor 0 Hi, I want to learn single-cell RNA seq analysis. I am looking for a tutor who can teach me the following open-access resources related to scRNA seq analysis – OSCA hemberg lab tutorial sanger lab tutorial etc. These would be hands on session where…

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Recruitment Of Postdoctoral Scholar in Cancer Biology/Cancer Genomics University of Chicago

EMPLOYER Northwestern University LOCATION Chicago, Illinois SALARY Commensurate with experience POSTED September 21, 2021 DISCIPLINE Life Sciences, Computational Biology, Genomics, Immunology Position Type Full Time ORGANIZATION TYPE Academia Job Type Postdoc Postdoctoral recruiting (experiential or computational) is available in murine and human innate immune interactions or precision medicine approach during the development of rheumatoid…

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Team Lead Comp Bio in Immunology & Respiratory job with Paramount Recruitment

Team Lead Computational Biology in Immunology & Respiratory – Germany Do you have experience in leading a team of computational biologists in immunology & respiratory? If so, then we have the perfect opportunity for you! One of our most highly respected pharmaceutical clients is now looking for a team leader…

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Compare gene expression between scRNAseq and bulk RNAseq data

Compare gene expression between scRNAseq and bulk RNAseq data 0 I have a scRNAseq dataset and a bulk RNAseq dataset. I want to compare the gene expression between the two datasets. Gene expression of these 2 datasets are at different scales. Is there a way to merge/scale/normalize these 2 datasets…

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Re-analysis of multiple scRNAseq data as a combined new one

Re-analysis of multiple scRNAseq data as a combined new one 0 Hi all, There are so many regions in brain.The cortex itself is of many types.I found many single cell RNA seq studies which focus on different regions eg- gse … somatosensory cortex dropseq year 2015 gse….. primary visual cortex…

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Principal Bioinformatics Scientist – Cell and Gene Therapy

Principal Bioinformatics Scientist – Cell and Gene Therapy Germany – Pharma The global Computational Biology and Digital Sciences (gCBDS) department is engaged in target discovery research and the application of innovative methods to resolve causative factors in disease progression. This is a great opportunity to lead computational projects in a…

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Rockefeller Disability Jobs – Director of Research Bioinformatics in New York, New York, United States

Job: IRC26893 Description Job Title Director of Research Bioinformatics Laboratory / Department Hospital Department Description The Rockefeller University Hospital is funded by the National Institutes of Health and has 20 patient beds for clinical research. The Hospital provides researchers with an opportunity to conduct clinical studies, and offers both normal…

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I downloaded fastq files from a repository and tried to run fastqc, how can the average sequence length be only 8 bp?

I downloaded fastq files from a repository and tried to run fastqc, how can the average sequence length be only 8 bp? 1 I downloaded sequencing files from 2 patients from here: www.ebi.ac.uk/ena/browser/view/PRJNA588461?show=reads there is one fastq file for the forward (1) and reverse (2) reads. I wanted to look…

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Ways to analyze treatment changes in scRNAseq

Ways to analyze treatment changes in scRNAseq 0 Hi, I am working with single cell RNA seq to determine gene expression changes in individual cells using two conditions: untreated and treated. I have merged the untreated and treated files into a single seurat object to generate featureplots of genes that…

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scRNASeq analysis Transcript abundance and gene abundance

scRNASeq analysis Transcript abundance and gene abundance 2 What is the code ,pipeline to get transcript abundance or gene abundance in cell type for scrnaseq data. Example – If pbmc data has different kinds of cells but I want to get gene abundance or transcript abundance for my gene of…

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R Bioconductor Courses

Listing Results R bioconductor courses Bioconductor Introduction To R / Bioconductor Harvard Bioconductor.org All Courses 016-05-16 Just NowIntroduction to R / Bioconductor. Buffalo, NY. 2016-05-16 ~ 2016-05-17. Instructors. Martin Morgan; Lori Shepherd; Description. This is a two-day course introducing R and Bioconductor for the analysis and comprehension of high-throughput genomic…

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How do I load a GEO dataset into Seurat?

How do I load a GEO dataset into Seurat? 1 I’m very new to single cell clustering, but have been able to get results from Seurat using sample datasets from 10x Genomics and also some datasets that were in H5 format. I’m looking for scRNA-seq datasets that are specific to…

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Research Scientist Bioinformatics at Exscientia

We are looking to hire an experienced bioinformatician who specializes in the analysis of human NGS data. The Research Scientist Bioinformatics will lead the development and expansion of our in-house NGS capabilities together with data managers and software developers, while also carrying out project-specific analyses. Exscientia GmbH is a company…

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infer type of single-cell chemistry from fastq

scRNAseq – infer type of single-cell chemistry from fastq 1 Hello all, it’s a known thing there’s lots of variants of single cell experiments – e.g. kb –list from kallisto-bustools lists at least 10 different variants. If you’re processing a reasonably big selection of scRNA-seq experiments, it would make sense…

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Bioconductor – scRNAseq

DOI: 10.18129/B9.bioc.scRNAseq     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see scRNAseq. Collection of Public Single-Cell RNA-Seq Datasets Bioconductor version: 3.11 Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. Author: Davide Risso…

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Bioinformatics Analyst in Pittsburgh, PA

Description Purpose: The UPMC Genome Center is a clinical grade, full-service, high-throughput genome center with sequencing options designed for both clinical and research needs. We are looking for members to join our Bioinformatics team for analysis of a wide spectrum (Whole Exome/Genome Germline and Somatic, RNAseq, scRNAseq) of NGS data…

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WNN (Seurat v4) vs. totalVI (scvi-tools) for CITE-seq data

WNN (Seurat v4) vs. totalVI (scvi-tools) for CITE-seq data 0 I want to build a UMAP from CITE-seq data with a joint embedding of the scRNA-seq and protein ab data. What’s the ‘best’ method in terms of representing the most accurate embedding? In the totalVI paper, they say totalVI >…

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should barcode in scRNAseq be deleted when demultiplexing

should barcode in scRNAseq be deleted when demultiplexing 1 I demultiplex fastq files using the demultiplex program ,and find the result didn’t delete barcode, I want to ask if it is necessary to delete the barcode in RNAseq. any suggestion is appreciated! demultiplexing scRNAseq • 128 views If you have…

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UMAP of TRA/B

Hello, I have output from a single cell sequencing run that has both the VDJ and gene expression data. For the same cells, we also used a hybrid capture approach to sequence the TCR sequences. I have compared the TCR sequences across the two approaches and I have found a…

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How to load Seurat Object into WGCNA Tutorial Format

As far as I can find, there is only one tutorial about loading Seurat objects into WGCNA (ucdavis-bioinformatics-training.github.io/2019-single-cell-RNA-sequencing-Workshop-UCD_UCSF/scrnaseq_analysis/scRNA_Workshop-PART6.html). I am really new to programming so it’s probably just my inexperience, but I am not sure how to load my Seurat object into a format that works with WGCNA’s tutorials (horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/)….

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Violion plot with statistics

Violion plot with statistics 0 Hi I am using Seurat for scRNA-Seq analysis. Along the analysis, i used Seurat’s VlnPlot function as the following: VlnPlot(Myeloid.object, features=”Mki67″, split.by = ‘Sample’, pt.size = 0) The feature is then represented in a different color for each Sample, and is divided by cluster. I…

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Team Lead Computational Biology in Immunology & Respiratory job with Paramount Recruitment

Team Lead Computational Biology in Immunology & Respiratory – Germany Do you have experience in leading a team of computational biologists in immunology & respiratory? If so, then we have the perfect opportunity for you! One of our most highly respected pharmaceutical clients is now looking for a team leader…

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Normalisation for single nuclei RNA-seq

Normalisation for single nuclei RNA-seq 0 For single cell RNA-seq the typical workflow includes a normalisation step to account for variable sequencing depth. In Scanpy/Seurat, CPM (Counts per million) is a simple and common choice. We don’t normally normalize for gene length (like we would with full length transcript bulk…

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Differential Gene Expression after batch correction with DESC?

Differential Gene Expression after batch correction with DESC? 0 I recently performed batch effect correction on single cell RNA-seq data with DESC. www.nature.com/articles/s41467-020-15851-3#Sec11 eleozzr.github.io/desc/ The batch corrected clustering and dimensional reduction worked well but I would like to determine differentially expressed genes between cell populations from two different batches. I…

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scRNAseq STAR create index how to set –sjdbOverhang

scRNAseq STAR create index how to set –sjdbOverhang 0 hello everyone, I want to create index before align read using STAR, the sjdbOverhang is described as ReadLength-1, so does it mean I should set 149 if the data is from Illumina 2×150bp? thanks scRNAseq STAR sjdbOverhang • 12 views Source…

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