Tag: scRNA

Which method works best for analysing ONE sample of scRNA-seq data?

Which method works best for analysing ONE sample of scRNA-seq data? 1 Hello, I currently have a single-cell RNA-seq (scRNA-seq) data of a single person (sample) and i want to perform DE analysis. However, when I run the DESeq() in the DESeq2 package, it shows an error about only one…

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Identification of a regulatory pathway inhibiting adipogenesis via RSPO2

Integration of APC scRNA-seq data reveals heterogeneity of adipocyte progenitor cells In a previous study9, we defined Lin−Sca1+CD142+ APCs as adipogenesis regulatory (Areg) cells and demonstrated that these cells are both refractory toward adipogenesis and control adipocyte formation of APCs through paracrine signaling. In contrast, Merrick et. al.4 observed that Lin−CD142+ cells…

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The Evolution of scRNA-seq Analysis

By Jane CookNovember 29, 2021 What Can scRNA-seq Data Tell Us? Single cell sequencing technologies have exploded in popularity for biological research over the last five years. The appeal of scRNA-seq lies in its specificity and scalability compared to older research techniques like Western blotting. Researchers can use scRNA-seq to…

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Decoding gene regulation in the fly brain

1. Li, H. et al. Classifying Drosophila olfactory projection neuron subtypes by single-cell RNA sequencing. Cell 171, 1206–1220 (2017). CAS  PubMed  PubMed Central  Google Scholar  2. Davie, K. et al. A single-cell transcriptome atlas of the aging Drosophila brain. Cell 174, 982–998 (2018). CAS  PubMed  PubMed Central  Google Scholar  3….

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Postdoctoral Scholar – Bioinformatics/Biomedical Data Science

The University of Nevada, Reno (UNR) appreciates your interest in employment at our growing institution. We want your application process to go smoothly and quickly. Final applications must be submitted prior to the close of the recruitment. If you need assistance or have questions regarding the application process, please contact…

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Postdoc Position in Bioinformatics in Stem Cell Neurobiology

DepartmentDepartment of Histology and Embryology  – Faculty of MedicineDeadline 28 Feb 2022Start date Jully 2022Job type full-timeJob field Science and research Medical Faculty of Masaryk University, Brno, Czech Republic, invites excellent scientists to apply for Postdoc position in Bioinformatics in Stem Cell Neurobiology   Description: The Department of Histology and Embryology is…

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Postdoc Position in Bioinformatics in Stem Cell Neurobiology job with MASARYK UNIVERSITY

Department Department of Histology and Embryology – Faculty of Medicine Deadline 28 Feb 2022 Start date Jully 2022 Job type full-time Job field Science and research Medical Faculty of Masaryk University, Brno, Czech Republic, invites excellent scientists to apply for Postdoc position in Bioinformatics in Stem Cell Neurobiology   Description: The Department of…

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About ‘Estimated Number of cells’ in snRNA-seq

About ‘Estimated Number of cells’ in snRNA-seq 0 Hi all, I am analyzing single nucleus RNA-seq data using Seurat. And I have total four group and 24 samples (Brain region A Control & case and Brain region B Control & case; each n=6). I wonder what is the appropriate range…

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Integrating Bulk RNA-seq data with Single cell RNA seq data

Integrating Bulk RNA-seq data with Single cell RNA seq data 0 Hello all, recently, I had been trying to integrate bulk RNAseq data into single-cell data where I treat each sample in my bulk RNAseq data as a single cell and integrate it into the single-cell data based on the…

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Is there a database of bioinformatics tools & databases?

All – Some years ago I was speaking to Sean Davis Re: the plethora of bioinformatics tools and databases. I commented to him that merely keeping up with what is available is difficult in the context of a full-time job, let alone mastering what you feel to be the best-in-class…

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NA values for mitochondrial gene percentage

NA values for mitochondrial gene percentage 0 I am running Seurat on publicly available dataset of ~400k cells. More than 80% of the cells are returned as NA when I use percentageFeatureSet(object, pattern = “^MT-“). How should I interpret these result? Does this mean the 80% of cells are of…

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Bioinformatics Scientist, Discovery Biology job with Surrozen

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…

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How do I access inflection points in Seurat object?

How do I access inflection points in Seurat object? 0 I ran the following code below to calculate inflection points for the UMI counts for my single cell data using Seurat. seurat_obj <- CalculateBarcodeInflections(seurat_obj,barcode.column = “nCount_RNA”,group.column = “orig.ident”,threshold.low = NULL,threshold.high = NULL) I want to obtain the inflection points so…

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Correct usage of FindConservedMarkers() in Seurat

Correct usage of FindConservedMarkers() in Seurat 0 Dear all, I have a Seurat object of a certain cell type with a UMAP of 7 clusters. I also have information about the sample’s origin (primary tumor/metastatic) in my metadata. Looking at the UMAP I can clearly see that clusters 1 and…

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Post Doctoral Research Associate Bioinformatics job with Beth Israel Deaconess Medical Center/Harvard Medical School

The Hide Lab at Harvard Medical School and BIDMC seeks a bioinformatics/computational biology postdoctoral fellow for training. We focus on target discovery, and diagnostic and therapeutic applications for Alzheimer’s Disease. The position is under the direction of Dr. Winston Hide (Systems RNA medicine) and is available immediately. For a list of publications…

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seurat, subcluster and trajectory analysis (Monocle 3)

seurat, subcluster and trajectory analysis (Monocle 3) 1 Hi all, I am analyzing single cell RNA-seq data using Seurat and would like the follow up the analysis with cell trajectory analysis using Monocle3. So I tried several methods, but I am not sure how to do it. I want to…

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Ph.D. Bioinformatics Specialist (Long-Term Contract) – NIH/NIEHS

Job:Ph.D. Bioinformatics Specialist (Long-Term Contract) – NIH/NIEHS – Research Triangle Park, NC 0 Kelly Government Solutions is a strategic supplier and business partner to the federal government and its key suppliers. We are seeking an individual to work as a Ph.D. Bioinformatics Specialist at the National Institutes of Health in…

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Error “start too small” when running htseq-count on a sorted .bam file

Error “start too small” when running htseq-count on a sorted .bam file 0 Hello, This is my first time aligning scRNA-seq reads to a reference genome to analyze differential gene expression. I am using htseq-count to obtain count files for my different samples and I am receiving the following error:…

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Why do some genes are more prone to dropout effect in scRNA-seq?

Why do some genes are more prone to dropout effect in scRNA-seq? 0 Dear Community, scRNA-seq analysis has its own conventions. For example, CD56 is a canonical protein marker for the identification of Natural Killer (NK) cells. However, in scRNA-seq analysis, NCAM1 (gene for CD56) is not commonly used. Instead,…

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vanheeringen-lab/seq2science – Giters

Seq2science is the attempt of the van heeringen lab to generate a collection of generic pipelines/workflows which can be used by complete beginners to bioinformatics and experienced bioinformaticians alike. Please take a look at our docs for help with installation, how to run it, and best practices. Our supported workflows:…

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No cell names (colnames) names present in the input matrix

CreateSeuratObject: No cell names (colnames) names present in the input matrix 2 I did scRNA-seq using patient PBMC, 4 biological replicates. Each PBMC was tagged with 4 different types of hashtag oligos and subjected to multiplexing. Using fastq files, cellranger multi was performed and 4 matrices were generated. Using Seurat,…

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The Biostar Herald for Tuesday, November 23, 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 Mensur Dlakic, Istvan Albert, and was edited…

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Seurat FeaturePlot blend and order

Seurat FeaturePlot blend and order 0 I am wondering if its possible to apply order = TRUE and blend = TRUE at the same time in FeaturePlot, because for the blended umap the ordering is still default. Basically bring the yellow dots up top. Thanks. FeaturePlot(Data.Combined.c3, features = c(“Gene1”, “Gene2”),…

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How to Analyze Read Counts datasets and UMI-Counts datasets in scRNA-seq

How to Analyze Read Counts datasets and UMI-Counts datasets in scRNA-seq 0 Hello! I am analyzing datasets with some having UMI-counts matrices, but some being read-counts matrices (they were sequenced with technologies that do not incorporate UMIs). According to this paper (UMI-count modeling and differential expression analysis for single-cell RNA…

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Is there a way to distinguish doublets from phagocytes performing efferocytosis in scRNA-seq data?

Is there a way to distinguish doublets from phagocytes performing efferocytosis in scRNA-seq data? 0 Hello everyone! Here is an interesting conundrum. It has been reported that phagocytes may contain so-called “passenger” transcripts that originate from engulfed apoptotic cells, which not only obscures the transcriptional profile of a true phagocyte…

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Asc-Seurat: analytical single-cell Seurat-based web application | BMC Bioinformatics

To demonstrate Asc-Seurat’s functionalities, we analyzed the publicly available 10× Genomics’ 3k Peripheral Blood Mononuclear Cells (PBMC) dataset [26], showcasing the analysis of an individual sample. In addition, we used a second PBMC dataset to demonstrate the analysis integrating multiple samples in Asc-Seurat. The second PBMC dataset was generated by Hang…

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Gene regulatory Network analysis using SCRNA-seq

Gene regulatory Network analysis using SCRNA-seq 0 Hi All, I am new to the scRNA_seq data analysis. Recently I analyzed a treatment vs control scRNA-seq. Treatment group has samples treated with a compound, which has shown positive effect (reduction in disease). Purpose of the study is to understand the mechanism…

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integrated scRNA-seq dataset

integrated scRNA-seq dataset 0 I read a lot of methods about integration of multiple scRNA-seq datasets from different cohorts, species, or experimental designs. I’m curious about a question. It seems that almost all of studies try to explore “methodology” of integration rather than “application”. Is there any publications using one…

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Principal Component Analysis Rna Seq

Listing Results Principal component analysis rna seq Genomatix Principal Component Analysis For RNASeq Data Preview 2 hours agoThis is explained in detail on “RNA–Seq workflow: gene-level exploratory analysis and differential expression”. The matrix of raw counts is input to the DESeq2 rlog function and the resulting transformed matrix is used…

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Comparing gene expression between biological replicates

Spatial transcriptomics analyses: Comparing gene expression between biological replicates 0 Hi everyone, I have 10X Visium mouse brain data for 4 different conditions – 3 replicates per condition and two tissue sections per mouse. I am trying to understand the best way to approach gene expression analysis given this data;…

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How to quickly find and filter coexpressed markers with one specific gene of interest in individual cells using scRNA-seq data?

Hello Biostars Community, How to quickly and precisely, find and filter coexpressed markers with one specific gene of interest in scRNA-seq data? Is there a way to do this, without making a gene-gene correlation matrix (takes wayyy too long)… Using clustering often just groups together cells with similar expression patterns,…

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sequencing – Plotting QC output for scRNA data analysis using Seurat R and accessing Seurat object data

I am new to R, and want to analyse some public scRNA seq data published in Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP et al. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Cell 2018 Nov 1;175 (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120575). I have tried to follow the online…

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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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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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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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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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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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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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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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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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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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“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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Biocmanager Install Vs Install Packages

Introduction to RNAseq I Day 3 Nicolas Rochette (EEB/ISG, UCLA) Karolina Kaczor-Urbanowicz (Oral Biology & Medicine, UCLA) UCLA Institute for Quantitative and Computational BiologyOver-representation (or enrichment) analysis is a statistical method that determines whether genes from pre-defined sets (ex: those beloging to a specific GO term or KEGG pathway) are…

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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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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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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 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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[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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