Category: scRNA

Seurat sctransform – does anyone know of a good explanation for biologists?

Seurat sctransform – does anyone know of a good explanation for biologists? 0 Hi, I was wondering whether anyone knows of a good blog/video/post explaining sctransform in a clear and easy to understand way. I understand the idea of the approach but would like to further understand the details. The…

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GEOquery with R

GEOquery with R 0 I am trying to start some analysis of RNA seq data with R. However, I am having some trouble with downloading the data. I have downloaded the following libraries: install.packages(“BiocManager”) install.packages(“forcats”) install.packages(“stringr”) install.packages(“ggplot2”) install.packages(“ggrepel”) install.packages(“readr”) install.packages(“tidyr”) install.packages(“survminer”) BiocManager::install(“GEOquery”) BiocManager::install(“limma”) BiocManager::install(“pheatmap”) BiocManager::install(“org.Hs.eg.db”) Ran this code: library(GEOquery) gse…

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Complexity of gene expression data in scRNAseq

2 hours ago esergison • 0 Hello, I’m a biologist trying to understand some scRNAseq data. I’ve been following this tutorial: github.com/hbctraining/scRNA-seq/blob/master/lessons/04_SC_quality_control.md I’m looking at dot plots of complexity that graph unique transcripts vs sequencing reads and I’m having trouble understanding what complexity means here. Is this a way of…

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some questions about sample, integration and subcluster

some questions about sample, integration and subcluster 0 Hi, every teacher, I’m new in scrna-seq and i had read some posts about scrna-seq, but there are several questions which make my confused: how to qualify a bad sample(not a cell),and should a bad sample be abandoned? i test 3 samples…

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Why only reverse fatsq file is used for mapping step in single cell RNA sequencing analysis?

Why only reverse fatsq file is used for mapping step in single cell RNA sequencing analysis? 1 Dear all, I am following a tutorial to do ScRNA-Seq analysis. In the mapping step it has been advised to use the reverse strand, however I don’t understand the logic behind this. Can…

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Review of popular science: analysis and comparison of single-cell RNA sequencing methods

Using 2i/LIF and ERCC inserted RNA cultured mouse embryonic stem cells (mESCs) as materials, using 6 different library preparation methods (CEL-seq2/C1, Drop-seq, MARS-seq, SCRB-seq, Smart-seq /C1 and Smart-seq2) prepare single-cell RNA-seq data. The difference between these methods lies in the use of unique molecular marker (UMI) sequences, which can distinguish…

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Researchers Submit Patent Application, “Immune Profiling Using Small Volume Blood Samples”, for Approval (USPTO 20210324447): Patent Application

2021 NOV 05 (NewsRx) — By a News Reporter-Staff News Editor at Insurance Daily News — From Washington, D.C., NewsRx journalists report that a patent application by the inventors Brown, David (Pasadena, CA, US); Dobreva, Tatyana (Pasadena, CA, US); Park, Jong Hwee (Pasadena, CA, US); Thomson, Matthew W. (Pasadena, CA,…

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analyzing spatial transcriptome data (Part 2)

Recognition of spatial variable features Seurat Two workflows are provided to identify molecular features related to tissue spatial location . The first is differential expression according to the pre labeled anatomical regions in the tissue , This differential expression can be determined by unsupervised clustering or a priori knowledge ….

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Advanced Bioinformatics Data Scientist job at BenevolentAI, November 2021

With over 35 nationalities and a range of backgrounds represented in our Benevolent team, we aim to build an inclusive environment where our people can bring their authentic selves to work, be respected for who they are and the exceptional work they do. We welcome and actively encourage applications from…

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Bioconductor – genomicInstability

DOI: 10.18129/B9.bioc.genomicInstability     Genomic Instability estimation for scRNA-Seq Bioconductor version: Release (3.14) This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of…

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The purpose of scaling to a negative binomial distribution in single cell RNA-seq

The purpose of scaling to a negative binomial distribution in single cell RNA-seq 1 Hi, I’m still a bit new to computational analysis of single cell data, but I’m doing my best to understand why things are done. As I understand it, when people cluster their data, typically they do…

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Bioconductor – TENxPBMCData

DOI: 10.18129/B9.bioc.TENxPBMCData     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see TENxPBMCData. PBMC data from 10X Genomics Bioconductor version: 3.11 Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics. Author: Kasper D. Hansen [aut], Davide Risso [aut], Stephanie Hicks [aut,…

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BioSpace hiring Bioinformatics Analyst/Computational Genomic Scientists in Frederick, Maryland, United States

COMPUTATIONAL GENOMIC SCIENTISTS & BIOINFORMATICS ANALYSTS * PROBLEM SOLVERS * ANALYTICAL THINKERS * COMMUNICATORSOPPORTUNITIES FOR COLLEGE GRADUATES & SEASONED PROFESSIONALSAre you passionate about using your talents to work on complex computational challenges in cancer, HIV and infectious diseases? Do you dream of working with renowned researchers using leading-edge genomics and…

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BAMboozle removes genetic variation from human sequence data for open data sharing

Strategy for stripping human sequence data of genetic information To lower the barriers in sharing sequence data, we propose, like others recently17, to remove information on genetic variation that could be used to infer the identity from aligned reads and compromises the privacy of the donor (Fig. 1a). Genetic variation, including…

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Bioconductor – Bioconductor 3.14 Released

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

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How to split hashtag fastq?

How to split hashtag fastq? 0 We have hashtag scRNA-Seq data (fastq1, fastq2, HTO-fastq1, and HTO-fastq2) each including 6 samples. We know that there are ways to calculate counts for each UMI for each sample (scRNA-seq CITE-seq-count bioinformatics). However, we would like to split the fastq files by the sample….

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To merge technical sequencing replicates or not to merge?

scRNA-seq: To merge technical sequencing replicates or not to merge? 0 HI all, I have sorted single cells in 10 96well plates and performed SmartSeq2. A couple of the plates had to be resequenced as the desired depth of 1Mreads/cell was not reached for a few of them. I am…

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CDSeq for deconvolution of whole blood RNAseq, any experience?

CDSeq for deconvolution of whole blood RNAseq, any experience? 0 Hello all, I am trying to infer the different cell types of my whole blood RNAseq experiment, as I can see there are a lot of tools available. I struggled past CDSeqR, which seems to be a new approach for…

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Postdoctoral Research Associate in Applied Bioinformatics at University of York

DepartmentA 2-year, fixed-term postdoctoral research associate position is available to work in the group of Dr Andrew Mason within the Jack Birch Unit for Molecular Carcinogenesis, part of the Department of Biology and York Biomedical Research Institute at The University of York. We are seeking a bioinformatics-focused researcher with a…

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Why ‘junk DNA’ is critical for our survival

Nearly half of our DNA has been written off as junk, the discards of evolution: sidelined or broken genes, viruses that got stuck in our genome and were dismembered or silenced, none of it relevant to the human organism or human evolution. But research over the last decade has shown…

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Single-Cell RNA Sequencing May Be Split By Parse Biosciences

When Alex Rosenberg, PhD, and Charlie Roco, PhD, were graduate students in Georg Seelig’s lab at the University of Washington, they drew out their idea for how to increase the scalablility of single-cell RNA sequencing (scRNA-seq) on a whiteboard. At that time, roughly five years ago, “large scale was about…

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Finding cluster specific markers in the Seurat object

Finding cluster specific markers in the Seurat object 0 Hello I have a basic question, I have done found top marker in the Seurat object, however using Violin plot shows this marker are not specific for the clusters. I used average expression function but it couldn’t help me for this…

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Re-analysis of multiple scRNAseq data

Re-analysis of multiple scRNAseq data 1 Hi all, Is it possible to recombine several old scRNA seq studies and answer a biological question i.e. build up a new analysis on the basis of combine analysis of old. EXAMPLE -I found many single cell RNA seq studies which focus on different…

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Bioinformatics Scientist II – 64019 Jobs in Philadelphia, PA – Children’s Hospital of Philadelphia

Location: LOC_ROBERTS-Roberts Ctr Pediatric Research Req ID: 113752 Shift: Days Employment Status: Regular – Full Time Job Summary The Bioinformatics Unit (BIXU) within the Center for Data Driven Discovery (D3b) at The Children’s Hospital of Philadelphia (CHOP) is seeking a level II Bioinformatics Scientist to join our over 30 professional…

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Odd-looking cell cycle scores in scRNA-seq data

Odd-looking cell cycle scores in scRNA-seq data 0 I’ve performed the cell cycle scoring using the scanpy workflow. When I visualise the phase I get the following plot: It seems that some cells have a vastly differing profile from the rest. Because of this, I can’t really tell if the…

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mitochondrial RNA percentage in bulk RNAseq data

mitochondrial RNA percentage in bulk RNAseq data 0 @335cd804 Last seen 16 hours ago United States Hi, I am analysing bulk RNAseq data of 86 samples by DESeq2. I really liked one feature of Seurat in scRNAseq analysis “mitochondrial content percentage” . Is there a simple way to extract “mt…

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General question about clustering in scRNAseq

I have recently finished an online scRNAseq course. I was a complete beginner in the field and I really enjoyed the course and have learnt a lot. Now that I have an overview of single cell, I have a flood of maybe dumb questions that escaped me during the course….

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How to identify the cell type computationally when you have a list of conserved cell type markers for mouse genome (as discovered by Seurat)?

How to identify the cell type computationally when you have a list of conserved cell type markers for mouse genome (as discovered by Seurat)? 0 I have a list of conserved cell type markers discovered from Seurat. I would like to annotate clusters with cell types based on that. For…

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KEGG passway analysis after Seurat analysis

KEGG passway analysis after Seurat analysis 0 Hello, everyone. I am so sorry for this amateur question. I have a scRNA-seq data and want to compare and visualize the expression levels across genes on a cluster by using clusterprofiler package (passway analysis), but I think the average expression levels of…

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Bioconductor – scDataviz

DOI: 10.18129/B9.bioc.scDataviz     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see scDataviz. scDataviz: single cell dataviz and downstream analyses Bioconductor version: 3.12 In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need…

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Editing Hash.ID in a Seurat Object

Editing Hash.ID in a Seurat Object 0 Hello, I integrated 12 samples that have following Seurats integration protocol here. These samples where each hashed based on their stimulation condition (two protein stimulations and one unstimulated). When I run DimPlot(Data_group1, reduction = “umap”, cols=pal, group.by = “hash.ID”) I get back a…

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Scientist II, Cancer Immunologic Data Commons

Scientist II, Cancer Immunologic Data Commons Dana-Farber Cancer Institute Boston, MA Full Time PTL Remote: 2-3 days remote/wk The Department of Data Science seeks a Scientist II to lead the development of the Cancer Immunologic Data Commons at Dana-Farber. The Scientist II will work closely with the laboratories of Drs.Franziska…

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If four groups (2 cell lines +/- treatments) of single cell RNA seq available, do I have to analyze each of the four datasets seperately?

If four groups (2 cell lines +/- treatments) of single cell RNA seq available, do I have to analyze each of the four datasets seperately? 0 I have our groups (2 cell lines +/- treatments) of single-cell RNA seq data. I used cellranger count and cellranger aggr to generated the…

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Different index than annotated genome scRNA-seq/troubleshooting : bioinformatics

Hi All, When pre-processing scRNA-seq data I have accidentally used different indexes (Hg19) for alignment in comparison to the gene annotation file I used for count quantification (GRCh38). I am using publically available data and my workflow seems to have achieved the same/better levels of alignment (~70%) than the original…

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Neuroscientists Roll Out First Comprehensive Atlas Of Brain Cells

When you clicked to read this story, a band of cells across the top of your brain sent signals down your spine and out to your hand to tell the muscles in your index finger to press down with just the right amount of pressure to activate your mouse or…

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So-Called Junk DNA Plays Critical Role in Mammalian Development

Nearly half of our DNA has been written off as junk, the discards of evolution: sidelined or broken genes, viruses that got stuck in our genome and were dismembered or silenced, none of it relevant to the human organism or human evolution. But research over the last decade has shown…

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Single cell RNA-seq analysis using a Galaxy interface

In this webinar, we will look at a Galaxy interface for single cell analysis. Specifically, we will run Scanpy (which would otherwise require Python programming skills) to analyse a Drop-seq dataset located in EMBL-EBI’s Single Cell Expression Atlas. Who is this course for? This webinar is aimed at individuals…

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use files with same name as input? : bioinformatics

Hi everyone, I have a question regarding the input of several fastq files into ‘CellRanger count’ pipeline.I performed scRNA-seq of different samples at a partner institute and the sequencing facility started by sequencing all the samples at a lower depth (to test the quality of the libraries) and only then…

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In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger?

In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger? 0 In single cell RNA-seq, do we perform regular quality checks and adapter trimming (just like in regular RNA-seq) before using cellranger? cellranger adapter_trimming QC scRNA-seq • 10 views • link 2 hours ago…

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GEO scRNA-seq entry with cell type information?

GEO scRNA-seq entry with cell type information? 1 Hello, I am trying to look for a scRNA-seq dataset hosted in GEO that, apart of the common files genes.tsv, barcodes.tsv and matrix.mtx, also has a file mapping barcode to cell types (as annotated by the paper). I have been trying to…

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How to perform sequence quality filtering of raw reads for single cell RNA seq?

How to perform sequence quality filtering of raw reads for single cell RNA seq? 0 I have a few single-cell RNA-seq samples (raw fastq reads). When I process raw reads, what should I do first? Is it demultiplexing? If so, what is the best tool I can use? Can I…

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use files with same name as input

Cell Ranger count pipeline: use files with same name as input 0 Hello, I have a question regarding the input of several fastq files into ‘CellRanger count’ pipeline. I performed scRNA-seq of different samples at a partner institute and the sequencing facility started by sequencing all the samples at a…

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UCD Bioinformatics Core Workshop

Prepare your environment for Monocle Create an RStudio project In the R console run the following commands to install the needed packages to run Monocle3 if (!any(rownames(installed.packages()) == “remotes”)){ if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“remotes”) } library(remotes) if (!any(rownames(installed.packages()) == “Seurat”)){ BiocManager::install(“Seurat”) } library(Seurat) if (!any(rownames(installed.packages()) == “R.utils”)){ BiocManager::install(“R.utils”)…

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Twice as many nFeature_RNA than nCount_RNA = more cell complexity? but how?

Twice as many nFeature_RNA than nCount_RNA = more cell complexity? but how? 0 Hi, I am re-analysing a publicly available single-cell RNA-seq dataset with two samples (plus minus treatment) and have downloaded preprocessed data from the geodataset as two .csv files. The authors state these files contain matrices that have…

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Why do we log transform and scale data prior to PCA for scRNA-seq analysis

Why do we log transform and scale data prior to PCA for scRNA-seq analysis 0 Hi, I have a query as to why it is necessary to both log transform, and center and scale, scRNA-seq data prior to performing PCA. I thought the purpose of both of these steps was…

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Bioinformatics Scientist, Discovery Biology – South San Francisco

Surrozen is a biotechnology company focused on discovering and developing novel regenerative medicines that unlock the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway.Surrozen was founded by five leading-edge scientists: K. Christopher Garcia, Ph.D., Roel Nusse, Ph.D. and Calvin Kuo, M.D., Ph.D. from Stanford…

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How to compare two Seurat object (sample) in order to find top markers?

How to compare two Seurat object (sample) in order to find top markers? 0 Hello, I have merged two Seurat object, they are not technical replicate, in fact they are different sample types. I have done integration using IntegrateData function in Seurat4. I have a question, how can I find…

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Is it ok to use z-scores means for inter-sample comparison?

Is it ok to use z-scores means for inter-sample comparison? 0 I have scRNA-seq from 2 patient. I want to show particular genes’ enrichment in both patients and compare them. So, first I integrated the datasets to be able to compare them. Then I want to compute the mean z-scores…

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BioSpace hiring Bioinformatics Scientist, Discovery Biology in South San Francisco, California, United States

DescriptionSurrozen is a biotechnology company focused on discovering and developing novel regenerative medicines that unlock the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway. Surrozen was founded by five leading-edge scientists: K. Christopher Garcia, Ph.D., Roel Nusse, Ph.D. and Calvin Kuo, M.D., Ph.D. from…

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Seeking a motivated bioinformatician

Job:Seeking a motivated bioinformatician 0 The Nephrogene lab at the Department of Nephrology, Medical University of Vienna, is seeking a motivated bioinformatician for a full-time position (www.meduniwien.ac.at/nephrogene/). The research focus is in the area of alloimmunity in kidney transplantation with a strong focus on genetic donor recipient incompatibility and changes…

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Dice hiring Associate Director Bioinformatics in Boston, Massachusetts, United States

Dice is the leading career destination for tech experts at every stage of their careers. Our client, Warman O’Brien, is seeking the following. Apply via Dice today! A leading innovative Biopharma who are focussing on the development of single-cell technology that offers molecular analysis of cells without the use of…

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October 2021 Galactic News – Galaxy Community Hub

Hello all, October brings Galaxy involvement in Hacktoberfest, and Outreachy, plus a nice batch of trainings, talksm and a Galaxy Papercuts CoFest day too. It also brings news of new job openings on two continents, two new platforms, blog posts (where My Little Pony makes an appearance, really), GTN updates…

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Does SCVI automatically use highly variable genes?

Does SCVI automatically use highly variable genes? 1 According to the SCVI tutorials, it is recommended to pre-select highly variable genes before training the SCVI model. Here is a piece of the code from here: docs.scvi-tools.org/en/stable/user_guide/notebooks/harmonization.html adata.layers[“counts”] = adata.X.copy() sc.pp.normalize_total(adata, target_sum=1e4) sc.pp.log1p(adata) adata.raw = adata # keep full dimension safe…

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cellranger count output does not give all genes.

cellranger count output does not give all genes. 0 Dear all, I have recently started using the cellranger from 10x for scRNA-seq data, after having used my own pipeline (with STAR alignment) for smart-seq2 data, to get the count matrix for then later analyzing with Seurat or Scanpy. I have…

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Research Scientist, Bioinformatics job with Gilead Sciences, Inc.

Research Scientist, BioinformaticsUnited States – California – Foster City Gilead Sciences, Inc. is a research-based bio-pharmaceutical company that discovers, develops and commercializes innovative medicines in areas of unmet medical need. With each new discovery and investigational drug candidate, we seek to improve the care of patients living with life-threatening diseases…

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Senior Bioinformatics Engineer job with Warman O’Brien

My client is a leading innovative Biopharma who are developing transformative T-cell receptor therapies to treat cancer and other immune-related diseases.   As the business continues to grow they are looking to add talented Bioinformatic Scientists and Engineers to their Translational Science team. If successful you will be joining a…

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Bioconductor – LRcellTypeMarkers (development version)

DOI: 10.18129/B9.bioc.LRcellTypeMarkers     This is the development version of LRcellTypeMarkers; for the stable release version, see LRcellTypeMarkers. Marker gene information for LRcell R Bioconductor package Bioconductor version: Development (3.14) This is an external ExperimentData package for LRcell. This data package contains the gene enrichment scores calculated from scRNA-seq dataset…

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Bioinformatics Scientist job with Warman O’Brien

My client is a leading innovative Biopharma who are developing transformative novel therapies to treat cancer and other immune-related diseases.   As the business continues to grow and obtain further funding to develop their pipeline, they are looking to add talented Bioinformaticians, at all levels, to their Translational Science team. If…

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“object ‘..sample_identity’ not found ” error in permutation_test with scProportionTest

Hi everyone, I’m new here and I’m also quite new in the world of scRNA seq analysis so I apologize for the mistakes in format I will probably make. I am analyzing some scRNA seq data, I have a dataset with 2 control animals and 2 mutants. I want to…

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Bioconductor Case Studies Use R

Bioconductor Case Studies Use R Analysing time course microarray data using Bioconductor MeV+R: using MeV as a graphical user interface for Omic association studies with R and Bioconductor (eBook Results: We describe RTNsurvival, an R/Bioconductor package that calculates regulon activity profiles…

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Comparative cellular analysis of motor cortex in human, marmoset and mouse

Statistics and reproducibility For multiplex fluorescent in situ hybridization (FISH) and immunofluorescence staining experiments, each ISH probe combination was repeated with similar results on at least two separate individuals per species, and on at least two sections per individual. The experiments were not randomized and the investigators were not blinded…

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Help in joint analysis of laser capture RNA-Seq with scRNA-Seq

Help in joint analysis of laser capture RNA-Seq with scRNA-Seq 0 I have RNA seq data that I captured using laser capture. the data is from a single cell layer of tissue from embryonic origin. I collected 16 samples from different locations of this layer from 4 different embryos (total…

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The Biostar Herald for Tuesday, October 05, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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Remove contamination across cell clusters

Remove contamination across cell clusters 0 I’ve got an scRNA-seq dataset filtered for immune cells. After applying the Seurat workflow I’ve discovered that some non-immune markers are expressed by cell subsets in almost all the clusters. See heat map: I’m fairly certain that those cells are contamination. How would you…

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Single cell RNA sequencing (scRNA-seq) in cardiac tissue

Introduction Cardiovascular diseases (CVDs) are the leading cause of death globally, taking an estimated 17.9 million (32.1%) lives in 2015, up from 12.3 million (25.8%) in 1990.1,2 CVDs are highly heterogeneous diseases involving a group of disorders of the heart and blood vessels, which include cardiomyopathy, hypertensive heart disease, heart…

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Network plot from expression data in R using igraph

[last update: January 27, 2020] igraph allows you to generate a graph object and search for communities (clusters or modules) of related nodes / vertices. igraph is utilised in the R implementation of the popular Phenograph cluster and community detection algorithm (used in scRNA-seq and mass cytometry), and also in…

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Bioinformatics Scientist in Diagenode – GrabJobs

Job Description Diagenode (a Hologic company) is an international biotech company that develops and commercializes innovative instruments and reagents systems for the life science research and molecular diagnostics. Founded in 2003, the Group is headquartered in Liège (Belgium), with subsidiaries in Denville (NJ, USA), in Toyama (Japan) and in Santiago…

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Bioinformatics Research Scientist

Bioinformatics Research Scientist – 93904 Organization: JG-Joint Genome Institute Lawrence Berkeley National Lab’s (LBNL, www.lbl.gov/) Joint Genome Institute Division (jgi.doe.gov/) has an opening for a Bioinformatics Research Scientist to join the team. In this exciting role, you will develop new computational methods to investigate gene regulation and regulatory sequence properties…

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Lab Officer

The Dorrity group at EMBL Heidelberg is seeking a highly motivated computational biologist to act as a Laboratory Officer, helping to set up a new lab that promotes a welcoming and positive atmosphere. Our group uses single-cell genomics as a whole-organism phenotyping tool in zebrafish to (1) understand how different…

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Postdoctoral Position in Immunotherapy, Virology, RNA Biology, Epigenetics, and Drug Design

– Advertisement – Postdoctoral Position in Immunotherapy, Virology, RNA Biology, Epigenetics, and Drug Design is available immediately for highly motivated recent Ph. Ds and/or MDs with strong training in any of the following disciplines: biochemistry, bioinformatics, immunology, molecular and cell biology, virology, medicinal chemistry or chemical biology to participate in the following projects…

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Bioconductor – LineagePulse

DOI: 10.18129/B9.bioc.LineagePulse     This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see LineagePulse. Differential expression analysis and model fitting for single-cell RNA-seq data Bioconductor version: 3.7 LineagePulse is a differential expression and expression model fitting package tailored to single-cell RNA-seq data (scRNA-seq). LineagePulse…

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Integrative analysis scRNAseq

Integrative analysis scRNAseq 0 Hi all, I am a begginer,exploring scrnaseq analysis. 1) If I combine say hypothetically various studies on cortex to see the transcript abundance and relative expression of a gene,can this be done? There would be much batch effect due to different libraries and location and year…

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How to show relabel sub cluster on the original cluster in Seurat

How to show relabel sub cluster on the original cluster in Seurat 0 Hi all! I have some data that I’ve been clustering using Seurat. I ended up with 30 clusters, but I subset 3 of these clusters are reclustered them in order to get more specific cell types. I…

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Lab Officer job with EMBL

The Dorrity group at EMBL Heidelberg is seeking a highly motivated computational biologist to act as a Laboratory Officer, helping to set up a new lab that promotes a welcoming and positive atmosphere. Our group uses single-cell genomics as a whole-organism phenotyping tool in zebrafish to (1) understand how different…

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Finding Subclusters in Seurat Clusters

Finding Subclusters in Seurat Clusters 1 I have performed clustering on my Seurat object and I would like to focus on one specific cluster and find study its subclusters. To do this, I understand that you have to subset the Seurat object. However, do I also have to run FindVariableFeatures()…

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Generating volcano plots of high and low expressed gene in scRNAseq data?

Generating volcano plots of high and low expressed gene in scRNAseq data? 0 Hi! I have scRNAseq data and I want to create DEG lists between cells with high expression of a gene vs. low. Ultimately, I would like to generate a volcano plot to visualize this and see co-expression…

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Associate Director Bioinformatics job with Warman O’Brien

A leading innovative Biopharma who are focussing on the development of single-cell technology that offers molecular analysis of cells without the use of complex instrumentation are looking to bring on a talented Principal Scientist or Associate Director of Bioinformatics/Computational Biology to drive the growth of their computational team.   Roles…

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Bioinformaticians (m/f/d) in Bioinformatics Core Unit

We are extending our bioinformatics team and are seeking for two enthusiastic bioinformaticians who would like to build and advance their career in translational cancer genomics and/or spearhead the implementation of next generation sequencing methodologies in routine cancer diagnostics and precision medicine. As a bioinformatician, you will conduct analyses of…

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scvelo latent time vs pseudotime

scvelo latent time vs pseudotime 0 Hi, I am doing RNA velocity and pseudotime analyses on my single-cell RNA-Seq datasets. For RNA velocity, I am using python’s scvelo package, which computes velocity as well as latent time. How is scvelo’s latent time different from pseudotime generated by packages like slingshot…

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How can I convert ensembl exon ID to gene symbol in a gene count dataframe?

How can I convert ensembl exon ID to gene symbol in a gene count dataframe? 1 I have an HTseq count file with a row containing exon ids and columns are exon counts. I need to convert them into gene IDs, given the fact that multiple exon ids may be…

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How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?

How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq? 1 Hey, I have tried harmony or CCA for batch effect correction for my single-cell RNA-seq data to compare the differeces between tumor and normal tissues, but I found that when I tried to integrate all…

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How can I convert ensemble exon ID to gene symbol in a gene count dataframe?

How can I convert ensemble exon ID to gene symbol in a gene count dataframe? 0 I have an HTseq count file with a row containing exon ids and columns are exon counts. I need to convert them into gene IDs, given the fact that multiple exon ids may be…

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[Q] Why do we need Normalization for scRNA-seq data? : bioinformatics

I am new to bioinformatics and currently try to understand why I should normalize scRNA-seq count data, e.g. by scaling each observation/cell to have the same number of total counts, before working with the data. This paper says that: “Thus, when gene expression is compared between cells based on count…

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Ttc30a affects tubulin modifications in a model for ciliary chondrodysplasia with polycystic kidney disease

Significance Cilia are tubulin-based cellular appendages, and their dysfunction has been linked to a variety of genetic diseases. Ciliary chondrodysplasia is one such condition that can co-occur with cystic kidney disease and other organ manifestations. We modeled skeletal ciliopathies by mutating two established disease genes in Xenopus tropicalis frogs. Bioinformatic…

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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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Regarding cellranger count and aggr functions

Regarding cellranger count and aggr functions 0 Here is the procedure I am following to do scRNA-Seq analysis. Can anyone please suggest to me whether it is correct or wrong? I have the fastq files for each sample name listed in the following format [Sample Name]_S1_L00[Lane Number]_[Read Type]_001.fastq.gz For example,…

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Which trajectory method is better !?

Which trajectory method is better !? 2 Hello I was engaged with a basic problem. I have dataset consist ~2000 cells and composed 8-9 clusters using Seurat package, then I transfer Seurat object to the Monocle. I tried monocle2 and monocle3. The problem is, how to make the trajectory ?…

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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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Aro Biotherapeutics hiring Investigator, Genetics & Bioinformatics in Philadelphia, Pennsylvania, United States

About Aro BioTx Join the team at Aro Biotherapeutics creating breakthrough biotherapeutics based on Centyrin oligonucleotide conjugates. Centyrins are small protein domains based on the fibronectin domains of human Tenascin C that combine the affinity and specificity properties of antibodies with the stability and tissue penetration properties of small molecules….

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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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cellranger count DETECT_COUNT_CHEMISTRY (failed)

cellranger count DETECT_COUNT_CHEMISTRY (failed) 0 I am learning scRNA-seq and the tutorial I follow uses dataset (1k pbmcs from healthy donor) from 10X genomics website. I downloaded fastq and reference transcriptome files and ran following command. cellranger-6.1.1/cellranger count –id pbmc_1k_v2_example –transcriptome /home/murat/Share/single_cell/refdata-gex-GRCh38-2020-A –fastqs /home/murat/Share/single_cell/pbmc_1k_v2_fastqs I get following message. Martian Runtime…

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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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Is it advised to use quantile normalization for scRNA-seq data?

Is it advised to use quantile normalization for scRNA-seq data? 0 I am currently developing an analytical tool for scRNA-seq data, and I am trying club couple of normalization techniques in that tool. Is it good to keep quantile normalization as an option for the user too? scRNA-seq quantile normalization…

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Omics data collection and merging of datasets from different studies

Omics data collection and merging of datasets from different studies 0 Hi! I’m going to do omics analysis on skin basal cell carcinoma. I’m currently trying to find publicly available data to use to make a data collection. I have looked after RNA-seq(high throughput) in GEO and found some studies…

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PC p values in JackStrawPlot in Seurat are not in order

PC p values in JackStrawPlot in Seurat are not in order 0 Hi, I got the Seurat object, then I did: pbmc <- JackStraw(pbmc, num.replicate = 100) pbmc <- ScoreJackStraw(pbmc, dims = 1:20) And when I did: JackStrawPlot(pbmc, dims = 1:15) The plot looks like this: As you can see,…

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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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Can SingleR be reused to identify cell types after subsetting the original Seurat Object

Can SingleR be reused to identify cell types after subsetting the original Seurat Object 0 Hi, I got a Seurat object and applied SingleR to identify cell types. Then subset the epithelial cell then redid the clustering on this cell type only. So now I got some new clusters. My…

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