Tag: scRNAseq

It seems like you can annotate all your cells as endothelial cells, problem solved 😉 But seriously, not clear what your expected cell types are (subtypes of endothelial cells perhaps) or the tissue type. If you can’t find a suitable reference dataset for the reference mapping approach, then you can…

ST. LOUIS — A Saint Louis University School of Medicine researcher says Type 2 inflammation, which is typically associated with allergies and asthma, is a risk factor for developing gastric cancer.  Rich DiPaolo, Ph.D., professor and interim chair in the Department of Molecular Microbiology and Immunology, warns that patients with…

ST. LOUIS — Stella Hoft, a M.D./Ph.D. student at Saint Louis University’s School of Medicine, was recently awarded a F30 Grant through the National Institute of Diabetes & Digestive & Kidney Diseases.  The four-year grant totals $207,008 and will support her research and training to become a productive, independent physician/clinician-scientist. …

P-value histogram of testLinearModel is not uniform 1 @lluis-revilla-sancho Last seen 10 hours ago European Union I’m analyzing a smart-seq dataset with samples from 9 different people with 4 runs and 17 plates. The samples were first treated and then sorted after stimulated with another condition, later were filtered in…

normalize for sample size in single cell rna seq cluster frequencies data 0 Hello, I have some single-cell RNA seq of different mice tissues and two different conditions (treated, untreated). After generating the UMAP plots and the resulted cells clusters I would like to calclute the frequency of treated vs…

What kind of statistical test does Cellranger count use? 1 Hi all, I’m trying to understand how 10X cellranger count/Loupe does clustering statistically. Is this a series of t-tests done one after another? Or by ANOVA? scRNAseq 10X Single-Cell • 164 views • link updated 2 hours ago by fracarb8…

integrate single cell RNA sequencing data 1 Good morning, In my project, the majority of the datasets use the Illumina HiSeq platform to process the data. However, I have come across one dataset that uses the NOVA sequencing platform, and I would like to include it. However, I am concerned…

DE genes across multiple scRNAseq clusters-are they significantly enriched? 0 I have a dataset comparing 2 samples. My experimental sample has thousands of differential expressed genes in each cell clusters. I am interested in looking at the genes that appear in multiple clusters to get a sense for genes and…

Biological resolution at the level of individual cells is powering the next phase of precision health. Developed by Honeycomb Biotechnologies, the HIVE™ scRNAseq Solution integrates sample storage and single cell profiling into a complete workflow, solving the issues that limit single cell RNA analysis by: Enabling multi-site and multi-timepoint sample…

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How to make a dotplot for bulk RNA average expression ? 1 Could any can tell, how to make a dotplot for average bulk RNAseq expression data ? I know how to do it with scRNAseq data, but I need to know how to do it for bulk RNAseq data….

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How to find marker genes for whole tissue from several different sub-tissue scRNAseq datasets 0 I’m trying to find the markers genes that distinguish cell types in a tissue (to use in predicting cell types) but am unable to find a scRNAseq dataset that covers all the cell types present….

News:course – single-cell RNAseq data analysis with R and Bioconductor 0 @info-21567 Last seen 13 hours ago Germany Dear all, The next edition of the online course “Single-cell RNAseq with R/Bioconductor course” will be in June 5th-9th. This course will introduce biologists and bioinformaticians to the field of single-cell RNA…

Job Posting #: 919696Position: Senior Bioinformatics Analyst Union: Non-UnionSite: Toronto Western Hospital (TWH) – Krembil Discovery TowerDepartment: Donald K. Johnson Eye Institute, Krembil Research InstituteReports to: Co-Director and Senior ScientistHours: 37.5 per weekSalary: $36.88 to $46.10 per hour commensurate with experience and consistent with UHN per hour commensurate with experience…

scRNAseq (bioconductor) data to seurat object 0 I am converting the scRNAseq data from bioconductor to Seurat object. I am not sure if my codes are correct. Thanks My input is: scRNAseq::PaulHSCData() paul <- PaulHSCData() paul_sce <- CreateSeuratObject(counts = counts(paul), meta.data = as.data.frame(colData(paul))) Warning: Feature names cannot have underscores (‘_’),…

How to analyze mars-seq single end-read scRNAseq data? 1 I am new to cellranger and mapping. I want to analyze a SRR2319344 scRNA-seq data which only has single-end read. But cellranger count requires paired end reads (R1 R2). May I ask how to analyze this SRA data? Thanks cellranger single-end…

cellranger count: an extremely low rate of correct barcodes was observed 1 I am new to cellranger. And I tried to run cellranger count for a fastq.gz file. My code is something like this: (** is just to replace my address name due to privacy issue) fastq-dump –outdir fastq –split-files…

Cell culture The MDA-MB231 (MB231) human breast cancer cell line was obtained from the American Type Culture Collection (ATCC, Manassas, VA) and grown in RPM1-1640 (Invitrogen) supplemented with 10% fetal bovine serum (FBS; Invitrogen, Waltham, MA) at 37 °C in a humidified atmosphere of 5% CO2 in the air. Cells were…

Research Alert Newswise — Glioblastoma (GBM) is the most aggressive glioma. Recently, immunotherapy using immune-checkpoint blockage (ICB) has provided therapeutic efficacy to various tumors. Despite an attractive ICB therapy, there have not been beneficial outcomes about GBM patients due to the characteristic of immunosuppressive environment. Thus, it is essential to…

Employer The team is studying the functional genomics of diseases involving the immune system. For this purpose, “omics” approaches (genomics, transcriptomics, scRNAseq, proteomics, etc.) are used to better understand the pathophysiology of these diseases. Our objective is in particular to develop new biomarkers allowing an earlier diagnosis of these immune…

How to combine a bulk and pseudobulk dataset? 0 @60367a29 Last seen 13 hours ago Belgium I am trying to merge two datasets (not data frames!) the first a bulk RNA sequencing datasets with two conditions and the second a pseudobulk dataset with 2 conditions. I need some help regarding…

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Downsampling of cells in scRNAseq DE analysis 0 Hello, this is a general question with no specific example concerning differential gene expression analysis in scRNAseq data. We sometimes want to compare two conditions in our DE** analysis but we see the the sample size of these groups greatly differ. For…

The laboratory of Dr. Claudia Jakubzick at Dartmouth Geisel School of Medicine is seeking highly motivated, independent postdoctoral researchers to join our team. Our lab is focused on investigating the role of mononuclear phagocytes in the immune system, with three main projects that require extensive investigation. These projects include: 1.  …

Error in colorRamp2(c(quantile(mean)[1], quantile(mean)[4], c(“white”, : argument “colors” is missing, with no default 0 col_AveExpr <- colorRamp2(c(quantile(mean)[1], quantile(mean)[4], c(“white”, “black”))) Error in colorRamp2(c(quantile(mean)[1], quantile(mean)[4], c(“white”, : argument “colors” is missing, with no default I am trying to make heatmap from sigs.df using complex heatmap, while making color code for average…

Hello! I’ve come across a really weird observation in the quality-control of my scRNAseq data that I really can’t explain. I am working on scRNAseq data of T cells, obtained with BD Rhapsody (microwell-based assay). We have several batches of sequencing (for biological replicates), and for some of them we…

DOI: 10.18129/B9.bioc.scMultiome   This is the development version of scMultiome; to use it, please install the devel version of Bioconductor. Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets Bioconductor version: Development (3.17) Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR…

How do I project known tSNE coordinates onto SeuratObject 1 I would like to analyze a published scRNAseq dataset by making a new Seurat Object. The authors have published their tSNE.1 and tSNE.2 coordinates in addition to all of their metadata but I cannot find how to create a tSNE…

Study cohort and performance during NMP An overview of the overall study population is presented in Table 1 (individual data are given in Supplementary Table 1). Detailed information on study livers and analysis is provided as workflow scheme in Fig. 1. The decision to apply NMP was based on one or a combination…

Low percentage of ‘Fraction Antibody Reads Usable’ in Feature Barcode Cell Ranger output 0 Hi, I have a question regarding the Cell Ranger output of scRNAseq with Feature Barcode. I’ve performed the standard Cell Ranger count using cellranger-6.0.0 and the following arguments: –id=A_GEX –libraries=library_A.csv –transcriptome=/……/refdata-gex-GRCh38-2020-A –feature-ref=/…../10x_feature_ref.csv When looking at the…

Do I need to specify the introns on the gtf file for cellranger? 0 Hello, I need to make a few changes to the human gtf file that I am using before building a reference and doing the alignment with cellranger. I made the changes to the exons but I…

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News:Single-cell RNAseq with R/Bioconductor course 0 Dear all, the next edition of the online course “Single-cell RNAseq with R/Bioconductor course” will be in June 5th-9th. This course will introduce biologists and bioinformaticians to the field of single-cell RNA sequencing. We will cover a range of software and analysis workflows that…

Bioinformatics Analyst II/III Job ID: req3427Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

Analysis a scRNAseq object that already has cell type annotation 0 Hi all I have recently downloaded a publicly available scRNAseq dataset that I want to analyse. The goal will be to do some differential expression analysis between two specific cell type clusters. The raw file was in .h5ad format,…

Error trying to run FindMarkers using future (in parallel) 0 Hi everyone, trying to run the FindMarkers function with Seurat running parallel using the future package (just got a mobile workstation with i9 12th gen processor and currently at 80gb ram) library(future) plan(multisession, workers = 24) options(future.globals.maxSize= 999999999999999999999999999999999999999999999999999999999999999) Cluster0 <-…

Demultiplex droplet single-cell RNA-seq data based on sex 0 Hi, There’s a bunch of tools exploiting SNPs to demultiplex scRNAseq data, i.e.: Vireo demuxlet fremuxlet scSplit Souporcell My Question is, do these tools work when pooling genetically identical samples, but of different sex (so actually not genetically identical), by means…

Alexandria, VA – The American Association for Dental, Oral, and Craniofacial Research (AADOCR) has announced the winners of the 2023 AADOCR Hatton Competition. The winners were recognized during the Opening Ceremonies of the 52nd Annual Meeting of the AADOCR, which was held in conjunction with the 47th Annual Meeting of the…

Seraut JackStrawplot PC1 0 Hi all, When I draw a jackstrawplot, I run into a same problem that the PC1 has non-significant p-value like this. How can I interpret this nonsignificant PC1? Any thoughts on that? Thank you very much 🙂 jackstrawplot Seurat scRNAseq PCA • 22 views • link…

cell density scRNAseq 0 Hello, I am new to scRNAseq data analysis. I am trying to understand the meaning of plotting cell density (contour plot). For example, the package scDataviz can plot/reveal the regions with high cell density but how should I interprete the results? what is the biological implication…

I can’t seem to find a clear answer to this question, so here it goes: I have sequenced scRNASeq + scVDJSeq (TCR) data, which has been sequenced using feature barcoding from 10x genomics, via antibody capture. There is a very useful cellranger multi command, which allows us to process both…

I can’t seem to find a clear answer to this question, so here it goes: I have sequenced scRNASeq + scVDJSeq (TCR) data, which has been sequenced using feature barcoding from 10x genomics, via antibody capture. There is a very useful cellranger multi command, which allows us to process both…

DOI: 10.18129/B9.bioc.scRNAseq   This is the development version of scRNAseq; for the stable release version, see scRNAseq. Collection of Public Single-Cell RNA-Seq Datasets Bioconductor version: Development (3.17) Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. Author: Davide Risso [aut, cph],…

Cellranger count with error information “… which wasn’t expected, or isn’t valid in this context” 1 Hello everyone, I just practiced the scRNAseq upstream analysis from cellranger official tutorial. But I met a small problem but it stopped me from going the next step. I followed the tutorial exactly but…

Scientists from the University of Hamburg, Germany, have developed a novel methodology, DiNiro, for unraveling differential regulatory disease mechanisms from single-cell RNA-seq data. Computational tools for analyzing differential gene expression profiles and differential pathway expression have been previously developed. DiNiro is the first known method based on single-cell data for…

How to get fraction of unspliced reads for specific gene from scRNAseq Cell Ranger output 0 Hi! I’m new to this forum (and to bioinformatics in general), so pardon my ignorance. I looked around and couldn’t find a similar question. I have the full Cell Ranger output (including BAM and…

Hello everyone I am working on spatial transcriptome data. I am following some tutorial (nbisweden.github.io/workshop-scRNAseq/labs/compiled/seurat/seurat_07_spatial.html#Subset_ST_for_cortex) for the QC, normalization and integration of multiple samples. After all analysis, I am interested in generating the feature-plot of desired set of genes. I used following two approaches : brain1 <- LoadData(“stxBrain”, type =…

Bioinformatics Analyst II/III Job ID: req3427Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research,…

scRNAseq package and cell type annotations 1 @0dc78e90 Last seen 4 hours ago Australia I would like to annotate or label UMAP clusters with cell types in a multiple myeloma single-cell RNA-seq dataset using the scRNAseq R package in conjunction with the SingleR package, if possible. I found a dataset…

About Us The South Australian Genomics Centre (SAGC). is a multi-institutional, national genomics and bioinformatics facility that is supported by Bioplatforms Australia (BPA) through the Australian Government’s National Collaborative Research Infrastructure Strategy (NCRIS). The SAGC has consolidated genomics and bioinformatics expertise in the state, with a group of ~10 genomics…

About Us The South Australian Genomics Centre (SAGC). is a multi-institutional, national genomics and bioinformatics facility that is supported by Bioplatforms Australia (BPA) through the Australian Government’s National Collaborative Research Infrastructure Strategy (NCRIS). The SAGC has consolidated genomics and bioinformatics expertise in the state, with a group of ~10 genomics…

DOI: 10.18129/B9.bioc.iSEE     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see iSEE. Interactive SummarizedExperiment Explorer Bioconductor version: 3.14 Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of…

Running AUCell on integrated scRNAseq data 1 Hi everyone, Posting here as I can’t quite seem to find a definite answer. I would like to assess cell-level pathway activity using AUCell on my integrated dataset. The vignette says to use the ‘data’ slot, which for me is a 3000 x…

STARsolo issue 0 hello, I’m performing STARsolo on pbmc fastq files and I’m using the reference genome from 10*genomics but I have this issu that I can’t understand (the reference genome is indexed) STAR version: 2.7.10b compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Mar 13 14:42:48 ….. started STAR run Mar 13 14:42:48 ……..

Pseudo-bulk celltype comparison across conditions from multiple-sources 1 @84e617fb Last seen 6 hours ago United Kingdom Hi all, I am aiming to merge my dataset with other available online. Data will be SCTv2 normalised, and visual integration will be done by Harmony. For DGE analysis, I would like to perform…

Integrating single-nucleus RNA-seq and single-cell RNA-seq datasets 0 Hi all, I am looking to integrate several scRNAseq datasets with a snRNAseq dataset. What are thoughts on integrating datasets from these 2 different modalities? Is it feasible/worth trying, or is it likely to do it poorly? Would appreciate it if you…

Filtering genes study-specific before Harmony integration? 0 Hello all, I have download two scRNAseq experiments from two different studies. After creating the seurat file using (features, matrix, counts), I removed the doublets, normalize these two samples using harmony and, in general, the result is pretty decent. However, there are some…

Check my understanding – difference between number of reads sequenced and Seurat nCount_RNA 0 I am reading a publication which has sequenced the 10x scRNA-seq library to around 50,000-100,000 reads / cell. When I performed QC and checked the nCount_RNA metric, the median nCount_RNA across all samples is around 3600….

I don’t think you can reduce the number of reads required for autodetection, and it would be a bad idea anyway, because the guess could go wrong. From 10X Q&A: TotalSeq B is specifically designed to be compatible with the Single Cell 3’ v3 and 3.1 workflows And from CellRanger…

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What is the purpose of Zero Inflated Models in single cell RNAseq 0 Hello, I read a paper about zero inflation (genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02601-5) but it leaves me in doubt for some points especially around the use of zero inflated models in the scRNAseq. I understood that the purpose of these models…

issue with merging single cell data files 0 I have 6 scRNAseq samples from 2 conditions including 3 treatments and 3 controls (from the same run and same experiment) and we have used 10X genomics. I have the samples in separate files in h5 format and trying to find a…

Summarizing permutation test/ bootstrap result for multiple samples for single-cell RNAseq data 0 I am trying to analyze single-cell RNAseq (more specifically spatial transcriptomics) data. I would like to calculate an index for an experimental condition. For example, I want to know if a particular gene is spatially enriched in…

Rust bioinformatics projects ideas 0 Hi everyone, I wish to work on a bioinformatics project to pick up Rust and to improve my computer science / programming knowledge in general. I don’t mind reinventing the wheel a little bit, since my main goal is to learn the language and demonstrate…

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CalcPerturbSig() Seurat: HELP 0 Hi, I have three conditions in my data (control and two mutants). I want to calculate pertubation scores for each mutant against control. Can I do that using CalcPerturbSig(). What parameters should I include in gd.class and nt.cell.class and split.by? singlecell differentialexpression Seurat scRNAseq • 19…

This is a bit of an XY problem but please go with it just for now. I have 10X scRNAseq I1, I2, R1 and R2 files. From these, I have extracted a subset of R2 reads into a subset.R2 file. I’ve also used filterbyname.sh to extract the same named subset…

Assuming you’re looking for differential expression values, the FindMarkers function within Seurat would be a good thing to try first: # find all markers distinguishing cluster 5 from clusters 0 and 3 cluster5.markers <- FindMarkers(pbmc, ident.1 = 5, ident.2 = c(0, 3), min.pct = 0.25) head(cluster5.markers, n = 5) ##…

Course: SINGLE-CELL RNA-SEQ ANALYSIS WITH R/BIOCONDUCTOR Dates: online, 5-9 June COURSE OVERVIEW This course will introduce biologists and bioinformaticians to the field of single-cell RNA sequencing. We will cover a range of software and analysis workflows that extend over the spectrum from the best practices in the filtering scRNAseq data…

Hello, I am currently using the hdWGCNA package on single cell data. So I get modules on a scRNAseq of cancer cells that I project on healthy cells in order to see what are the modules that are “absent” from the healthy cells and so “exclusive” to cancer cells. To…

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How to remove a gene before making a cellranger reference? 1 Hello, I was asked to make a new reference where I remove one of the genes from a reference and add some isoforms. I have found several instances of this gene in the gtf file and I will remove…

10x genomics hashtag antibody (biolegend) 1 Hello. I have 10x genomics single cell RNA sequencing data (fastq format), and I want to know the hashtag antibody (biolegend) sequence. Could you tell me how to read that? Thank you. Biolegend hashtag antibody scRNAseq 10x genomics • 52 views • link updated…

Error while converting ExpressionSet format to SingleCellExperiment format? 0 I encountered an error while trying to convert one ExpressionSet to SingleCellExperiment. I used the function of toSingleCellExperiment from Scater, however it gave me the error as below: scRNAseq.sce <- toSingleCellExperiment(SCEset) Error in toSingleCellExperiment(scRNAseq.eset) : methods::is(object, “SCESet”) is not TRUE Any…

I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it. I did the below: bulk_de_genes_up_list = bulk_de_genes[‘Gene’].tolist() # Subset the data…

Background. Oxidative stress (OS) can either lead to leukemogenesis or induce tumor cell death by inflammation and immune response accompanying the process of OS through chemotherapy. However, previous studies mainly focus on the level of OS state and the salient factors leading to tumorigenesis and progression of acute myeloid leukemia…

This has been debated for a few years now as the “dropout” problem, which is actually a mixture of different issues. On one hand, you are sequencing a relatively low input at a depth that does not reach saturation (i.e. you don’t measure all there is to measure). This is…

Start Current SNIC Medium Storage Projects SNIC 2022/6-148 In situ sequencing and scRNAseq JHL SUPR uses JavaScript for certain functions. We cannot guarantee that you will be able to use the system with JavaScript disabled. Primary Classification: 30108: Cell and Molecular Biology Secondary Classification: Allocation Abstract In situ sequencing is…

The electron transport chain (ETC) activity in mammalian cells is necessary for survival and proliferation. The ETC is composed of ~100 subunits mostly encoded in the nuclear genome, but 13 essential subunits are in the mitochondrial genome (mtDNA). Accumulation of mutations in the mtDNA can lead to severe genetic defects…

Hello, I analyzed some data using scanpy and now I want to do some pathway analysis. I have done DE analysis between each cluster and the rest and I want to do the pathway analysis for each cluster but I have a few questions. I initially followed the instructions from…

Merging FASTQs from the same sample 0 Hello, I have a question regarding merging FASTQ files from the same sample but different sequencing runs. We generated cDNA libraries using the 10X v3 protocol but weren’t sure they had worked so initially sequenced only a small fraction of the library (10,000…

SUMMARY In the lesioned zebrafish retina, Müller glia produce multipotent retinal progenitors that generate all retinal neurons, replacing lost cell types. To study the molecular mechanisms linking Müller glia reactivity to progenitor production and neuronal differentiation, we used single cell RNA sequencing of Müller glia, progenitors and regenerated progeny from…

Job Posting for Scientist II, Bioinformatics at PTC Therapeutics, Inc. Job Description Summary: The Scientist II, Bioinformatics is responsible for planning and performing scientific experiments that contribute to PTC’s research and drug discovery activities. The Scientist II is also responsible for communicating experimental results to his/her supervisor and…

REQUIRED SKILLS AND EXPERIENCE 1. Fluency in one programming and one scripting languages is required (Python, R/Matlab/Splus, Perl, Java) 2. Experience in developing algorithms for analysis of biological data. Experience in algorithm development for analysis of massively parallel sequencing data (NGS seq, RNA-seq/scRNAseq etc..) is highly desirable. 3. A track…

A new bioinformatic pipeline to investigate single cell eQTL analysis is now offered in the sequencing service from Singleron Biotechnologies. COLOGNE, Germany, Jan. 25, 2023 /PRNewswire/ — Bioinformatic experts at Singleron Biotechnologies, a leader in single cell sequencing, have developed a new single cell eQTL analysis workflow that takes advantage of…

A new bioinformatic pipeline to investigate single cell eQTL analysis is now offered in the sequencing service from Singleron Biotechnologies. COLOGNE, Germany, Jan. 25, 2023 /PRNewswire/ — Bioinformatic experts at Singleron Biotechnologies, a leader in single cell sequencing, have developed a new single cell eQTL analysis workflow that takes advantage of…

Run the usual steps including clustering and visualization via something like UMAP and then color the UMAP by these four markers. That assumes that the surface marker separation you see in flow holds true on a transcriptional level which is not necessarily the case. For example, hematopoietic surface-defined populations such…

Tools/pipeline for analysis of smart-seq3 data 1 I have Smart-Seq3 data and zUMIs refuses to work. Is there any other alternative? Nf-core pipelines rnaseq and scrnaseq doesn’t support sm3 yet. I am also prepared to go down the manual route. Has anyone tried umi_tools or alevin at least to demultiplex…

Change sample ID in BAM file to cell barcode 0 Hi all. I have a BAM file from one 10X scRNAseq sample. I want to try a tool out which was designed for a different type of data. The input for this tool is the output from samtools mpileup. samtools…

In a recent study posted to the bioRxiv* preprint server, researchers evaluated the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the peripheral nervous system (PNS). Study: Human iPS cell-derived sensory neurons can be infected by SARS-CoV-2 strain WA1/2020 as well as variants delta and omicron. Image Credit:…

The following is a summary of “Ewing Sarcoma and Osteosarcoma Have Distinct Immune Signatures and Intercellular Communication Networks” published in the November 2022 issue of Clinical Cancer by Cillo et al. Adolescents are disproportionately affected by the principal bone sarcomas, Ewing sarcoma, and osteosarcoma. The prognosis is very poor for…

Prepare Antibody Mix Supernatant • Add appropriate/manufacturer’s recommended amount of antibody-oligonucleotide conjugates to a 1.5-ml microcentrifuge tube. • If using a custom lyophilized antibody: Resuspend the antibody-oligonucleotide conjugates in an appropriate volume of labeling buffer. • Centrifuge the mix at 14,000 rcf for 10 min at 4°C. • Transfer the supernatant…

COMPANY MISSION At eGenesis, we aspire to deliver safe and effective human transplantable cells, tissue and organs utilizing the latest advancements in genome editing.  POSITION SUMMARY We are seeking a skilled Bioinformatics software engineer to join our thriving computational biology team. In this role, you will lead development of reproducible…

Let’s imagine a single cell experiment in which we have 3 biological replicates, treated (TR) and untreated (UNT). After all the necessary filtering and integration steps, we isolate a cluster of interest (cluster X), for which we want to test differential gene expression (DE) between TR and UNT. Ideally one…

recommend tools for scRNAseq cell type annotation 1 Dear all, May I know if there are recommended tools/webs for the cell type annotation? Say, I have the cell expression matrix, and want to generate a cell type/labels file based on the expression matrix and the prior knowledge of the cell…

I’m reading through this paper: Baran, Y., Bercovich, A., Sebe-Pedros, A., Lubling, Y., Giladi, A., Chomsky, E., … & Tanay, A. (2019). MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions. Genome biology, 20(1), 1-19. Maybe I am not familiar with this notation but I don’t understand the regularization…

About the job Our Team: Artificial Intelligence (AI) and Machine Learning (ML) algorithms can significantly speed up drug discovery and shorten drug development and identification of patients for clinical trials thereby creating better medicines that save lives. AI and Deep Analytics (AIDA) is a critical group in Data and Data…

How to convert single-cell RNAseq filename.mtx.gz to seurat object 0 Hi All, I need your great help with my public scRNAseq data obtained from GEO dataset analysis. For example, if I want to access this dataset (GSE118019) to convert it into Seurat object? There is no separate barcode, features, matrix…

How much RAM for scRNAseq 200K cells? 0 Hi all, Sorry if this has been asked multiple times before – I’m wondering what’s possible in the current landscape of bioinformatics tools. I’m planning on sequencing a set of 200,000 cells or so using 10X’s fixed RNA profiling technology. I’d like…