Tag: scRNA

Bioconductor – SCArray.sat

DOI: 10.18129/B9.bioc.SCArray.sat   Large-scale single-cell RNA-seq data analysis using GDS files and Seurat Bioconductor version: Release (3.17) Extends the Seurat classes and functions to support Genomic Data Structure (GDS) files as a DelayedArray backend for data representation. It relies on the implementation of GDS-based DelayedMatrix in the SCArray package to…

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Set up label.color with the same colors as the cluster colors in Seurat DimPlot() ?

Set up label.color with the same colors as the cluster colors in Seurat DimPlot() ? 1 Hello, I want to show on my UMAP, using the DimPlot() function, the same colors on the text labels as the cluster colors. If I set up the same colors in the same order…

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sNucConv: A bulk RNA-seq deconvolution method trained on single-nucleus RNA-seq data to estimate cell-type composition of human subcutaneous and visceral adipose tissues

Abstract Deconvolution algorithms rely on single-cell RNA-sequencing (scRNA-seq) data applied onto bulk RNA-sequencing (bulk RNA-seq) to extract information on the cell-types composition and proportions comprising a certain tissue. Adipose tissues cellular composition exhibits enormous plasticity in response to weight changes and high variance at different anatomical locations (depots). However, adipocytes,…

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To explore intratumor-heterogeneity of CLL_24 using single-cell multi-omics approach, we generated single-cell CITE-seq data for CLL_24, coupling scRNA-seq and protein surface marker measurements with oligo-tagged antibodies.

Dataset Description To explore intratumor-heterogeneity of CLL_24 using single-cell multi-omics approach, we generated single-cell CITE-seq data for CLL_24, coupling scRNA-seq and protein surface marker measurements with oligo-tagged antibodies. To explore intratumor-heterogeneity of CLL_24 using single-cell multi-omics approach, we generated single-cell CITE-seq data for CLL_24, coupling scRNA-seq and protein surface marker…

Continue Reading To explore intratumor-heterogeneity of CLL_24 using single-cell multi-omics approach, we generated single-cell CITE-seq data for CLL_24, coupling scRNA-seq and protein surface marker measurements with oligo-tagged antibodies.

scrna pipeline

scrna pipeline 0 I have 2 fastq files and did their quality check through fastqc tool. Which other steps do I need to do to complete the pipeline? scRNA-seq • 45 views • link updated 2 hours ago by Ram 39k • written 3 hours ago by anasjamshed ▴ 120…

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Postdoc Researcher – Single cell RNA-sequencing of plant defences against aphids

Category Research / Academic Location Wageningen Your JobAre you a talented postdoc with a passion for unraveling plant resistance mechanisms against aphids at the cellular level? Do you want to work in a multidisciplinary team along with experienced researchers in collaboration with plant breeding and biocontrol companies? If so, we…

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Cluster/group samples based on scRNA data

Forum:Cluster/group samples based on scRNA data 0 Hi all, I have ~50 samples with each being profilied by scRNA. By UMAP of each individual sample, I can clearly see 3-4 distinct patterns among these samples. Now what is the appropriate way for me to group these samples according to their…

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scRNA-seq CITE-seq-count bioinformatics

CITE-seq is a nice method of multiplexing single cell libraries using antibodies. Details here: cite-seq.com/ Although software exists, we found the exact methods very unclear so would like to present them here Many of these details have been adjusted from these discussions: github.com/Hoohm/CITE-seq-Count/issues/5 Terminology: hto: hashtag mRNA – read 2…

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Remove cells from Seurat based on a list

Remove cells from Seurat based on a list 2 Hi guys, is there a way to remove from Seurat3 object (all slots) a set of cells listed in a vector? I tried: my_object_without_cells = subset(object = my_dataset, cells = cells_to_be_removed) but the cells are still there. I checked the n…

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Moffitt Cancer Center hiring RSCH DATA ANALYST I BIOINFORMATICS in Tampa, Florida, United States

At Moffitt Cancer Center, we come face-to-face with cancer every day, but we also see courage. And it inspires us to be the safest and best place for cancer care – to bring greater hope to every patient we serve. It’s why we’ve been continually named One of the Top…

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Augusta University hiring Director, Bioinformatics – Immunology Center of Georgia in Augusta, Georgia, United States

About UsAugusta University is Georgia’s innovation center for education and health care, training the next generation of innovators, leaders, and healthcare providers in classrooms and clinics on four campuses in Augusta and locations across the state. More than 9,000 students choose Augusta for educational opportunities at the center of Georgia’s…

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How to label clusters from a UMAP

How to label clusters from a UMAP 0 So this is a broad question that I was hoping someone could shed some light on. I have a Visium tissue data set which I’ve clustered using scanpy, and for each tissue slice I usually get 5 or 6 resulting clusters. I…

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Staff Scientist – Translational Bioinformatics

Job Description About City of Hope City of Hope’s mission is to deliver the cures of tomorrow to the people who need them today. Founded in 1913,City of Hopehas grown into one of the largest cancer research and treatment organizations in the U.S. and one of the leading research centers…

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The genetics of neurogenic inflammation in rosacea

A recent study published in Nature Communications identifies rare genetic variants in families with rosacea. Study: Whole genome sequencing identifies genetic variants associated with neurogenic inflammation in rosacea. Image Credit: STEKO / Shutterstock.com What is rosacea? Rosacea is a chronic skin disorder that is characterized by erythema, flushing, telangiectasia, hyperplasia, pustules/papules, or…

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Clinical cohort for cancer sequenced using scRNA-Seq

Clinical cohort for cancer sequenced using scRNA-Seq 0 Just curious about the availability of single-cell RNA-Seq data with clinical attributes. All the transcriptomic data I found for the patients which have clinical parameters is bulk RNA-Seq. So is there any patient cohort (I might have missed in my search) for…

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Annotating Cluster in scRNA-seq – Scanpy

Annotating Cluster in scRNA-seq – Scanpy 0 Hello all, I am learning scRNA-seq using Scanpy and in the downstream analysis, after clustering the genes are ranked for each cluster. Now the next step is to annotate these clusters. But in the tutorial, they have annotated the clusters manually. Is there…

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Define conditions based on high or low gene expression for scRNAseq analysis

Define conditions based on high or low gene expression for scRNAseq analysis 0 Hello everyone, I am a beginner in single cell RNA sequencing analysis. I really need your help. I am wondering how I can group my scRNA data according to high and low gene expression (i.e. HighPD1/LowPD1) and…

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Presence of ribosomal gene / mitochondrial gene enrichment in each cluster of scRNA seq analysis

Presence of ribosomal gene / mitochondrial gene enrichment in each cluster of scRNA seq analysis 1 Hello Everyone, recently I have been working on the scRNA seq analysis of HBV-associated Heptatocellular carcinoma (HCC) cells using Seurat packages. When I used the 20 genes with lowest adjusted p-value in each cluster…

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Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues

Abstract Single-cell RNA sequencing (scRNA-seq) is invaluable for profiling cellular heterogeneity and dissecting transcriptional states, but transcriptomic profiles do not always delineate subsets defined by surface proteins, as in cells of the immune system. Cellular Indexing of Transcriptomes and Epitopes (CITE-seq) enables simultaneous profiling of single-cell transcriptomes and surface proteomes;…

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How to obtain cell-cell interaction list

How to obtain cell-cell interaction list 0 Hi, im doing Ligand-receptor interaction analysis with single cell data. I have two questions. 1) there are several ligand-receptor databases. How can i combine these databases and use that for LR interaction? 2) after cell-cell interaction analysis, how to obtain final results including…

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Housekeeping genes scRNA seq

2 hours ago bioinformatics ▴ 10 Hello, I am trying to follow this workflow for scRNA seq analysis. broadinstitute.github.io/2020_scWorkshop/data-wrangling-scrnaseq.html#filtering-low-quality-cells I have loaded the data and computed the percentage of mitochondrial genes for each cell However, the next step is to load a list of housekeeping genes. A file I do…

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scrna seq analysis – doublets

scrna seq analysis – doublets 0 Hello, I am trying to perform scrna seq analysis in R using this workflow www.singlecellcourse.org/single-cell-rna-seq-analysis-using-seurat.html I have tried to enter this code, however I do not have the file? Do you know what this file is or how I can create one? doublets <-…

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Single-cell Bioinformatics Scientist job with Zafrens, Inc.

Zafrens, Inc., a cutting-edge biotechnology company that is trying to redefine lifesciences product development, is seeking a Single-cell Bioinformatics Scientist. This is a great opportunity for someone with a passion for bioinformatics and an interest in innovative product development to work with a team of creative and adventurous scientists who…

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Construction of a circRNA-lincRNA-lncRNA-miRNA-mRNA ceRNA Regulatory Network Identifies Genes and Pathways Linked to Goat Fertility

Farzad Ghafouri1, Mostafa Sadeghi1*, Abolfazl Bahrami1*, Masoumeh Naserkheil1, 2, Vahid Dehghanian Reyhan1, Arash Javanmard3, Reza Miraei-Ashtiani1, Soheila Ghahremani4, Herman W. Barkema5, Rostam Abdollahi-Arpanahi1 and John P. Kastelic5 1University of Tehran, Iran 2National Institute of Animal Science, Republic of Korea 3University of Tabriz, Iran …

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Can we compare bulk RNAseq samples and single cell rnaseq clusters?

Can we compare bulk RNAseq samples and single cell rnaseq clusters? 2 Hi folks, I have 3 Bulk RNAseq samples from immune cells (Naive, Population1 and Population2), similarly I have two other immune populations from Single Cell RNAseq samples. I am interested in comparing 3 Bulk RNAseq and 2 single…

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scRNA-seq subclustering

scRNA-seq subclustering 0 Hi, I’m doing single cell data analysis with controls and disease samples. and it turned out that an specific cell type “A” is increased in disease condition. then i wanted to re-clustering (subclustering) only the A cluster, so that i find out which specific cell subtype is…

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“GGGGGGGG”I7 index read in my scRNA-seq library

“GGGGGGGG”I7 index read in my scRNA-seq library 0 Hello~ When I was analyzing scRNA-seq data generated from my customized platform. I always found “GGGGGGGG” I7 index read in the header. I designed the I7 index read as my cell barcode, so they should be different 8bp sequences. However, when I…

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scRNA-seq dataset comparison

scRNA-seq dataset comparison 0 Hi everyone,I am recently analyzing a scRNA-seq dataset X. After clustering and annotation, I have my landscape A.Next, I want to compare my scRNA-seq clusters with a public dataset Y. I have tried two methods, One is directly integrating datasets X and Y using Seurat IntegrateData…

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scRNA seq analysis – how to label cell types from clusters

2 hours ago bioinformatics &utrif; 10 Hello, I have followed this tutorial/workflow and managed to create a UMAP plot with labelled clusters (1-12 using the patient 1 of GSE162454 dataset from NCBI): holab-hku.github.io/Fundamental-scRNA/downstream.html#run-non-linear-dimensional-reduction-umaptsne However, the tutorial did not show how to create a UMAP plot with cell types labelled using…

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Isolation and Transcriptome Analysis of Plant Cell Types

The feasibility and effectiveness of high-throughput scRNA-seq methods herald a single-cell era in plant research. Presented here is a robust and complete procedure for isolating specific Arabidopsis thaliana root cell types and subsequent transcriptome library construction and analysis. Transcriptome analysis on single cell or cell types can detect the subtle…

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Bioinformatics Scientist job with Active Motif

Position Title: Bioinformatician Scientist Classification: Exempt Reports To: TBD Who is Active Motif? Active Motif is the industry leader in developing and delivering innovative tools to enable epigenetics and gene regulation research. We are committed to providing the highest quality products and superior service & support to serve the life…

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nf-core/marsseq: systematic pre-processing pipeline for MARS-seq experiments

Abstract As a result of advancing single sequencing technology (scRNA-seq), it has become possible to study gene regulatory mechanism(s) and their influence on evolving cell states in time at the level of individual cells. Since 2009, numerous scRNA-seq protocols have been developed, each with its own advantages, disadvantages and library…

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Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells

Stewart, J. B. & Chinnery, P. F. Extreme heterogeneity of human mitochondrial DNA from organelles to populations. Nat. Rev. Genet. 22, 106–118 (2021). Article  CAS  PubMed  Google Scholar  Stewart, J. B. & Chinnery, P. F. The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease. Nat. Rev. Genet….

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Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis

Tandem duplications and noncoding SNVs at the HCFP1 locus We enrolled families and simplex cases with nonsyndromic congenital facial paresis (CFP, cohort 1 US-based study) and performed genome-wide single-nucleotide polymorphism (SNP) analysis and whole-exome sequencing (WES) in two large dominant pedigrees, family 1 (Fam1) and family 9 (Fam9; Fig. 1a)….

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annotating single-cell cluster from Drosophila melanogaster using SingleR?

annotating single-cell cluster from Drosophila melanogaster using SingleR? 0 We have a data set from Drosophila melanogaster, we don’t know much about. We ran the Seurat-workflow and got various clusters. I would like to try and annotate this clusters in an automated manner. I know the SingleR package is the…

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Global Genome Editing Market: Rapid Growth Expected to Reach USD 15.7 Billion by 2032

The global genome editing market size was USD 3.8 Billion in 2022 and is expected to reach USD 15.7 Billion by 2032, and register a rapid revenue CAGR of 15.2% during the forecast period. According to the latest report by Reports and Data, the global Genome Editing Market size was…

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How to estimate the computing power needed for scRNA-seq

How to estimate the computing power needed for scRNA-seq 0 I am planning to perform a scRNA-seq analysis of a few million cells collected from various experiments. However, I need to estimate what computational power will be approximately needed to process bam and fastq files up to the DEGs, UMAPs,…

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How to add VDJ clonotyping data to Seurat object of scRNA-seq

How to add VDJ clonotyping data to Seurat object of scRNA-seq 0 I have performed CITE-seq (ADT, GEX, TCR) in 20 PBMC samples, consisting of responders and non-responders. By following Seurat tutorial, I performed standard pre-processing process, merging seurat object, integration, and drew the UMAP and compared the freq. of…

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ambient RNA quality control in scRNA-seq

ambient RNA quality control in scRNA-seq 0 Hi all, In scRNA-seq analysis, nCount_RNA and nFeature_RNA value of one sample is very high compared to other samples. (below figure) Also, ‘Fraction Reads in Cells’ in this sample are 70.1%, but do not have a steep cliff in this sample’s web summary…

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Bioinformatics Scientist – Active Motif Inc

Position Title: Bioinformatician Scientist Classification: Exempt Reports To: TBD Who is Active Motif? Active Motif is the industry leader in developing and delivering innovative tools to enable epigenetics and gene regulation research. We are committed to providing the highest quality products and superior service & support to serve the life…

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Annotation of spatial data

Annotation of spatial data 0 Hi, I have data for mouse tissue sections using 10x visium. But I don’t have the corresponding single cell RNA seq data for the same tissue. There are no publicly availble scRNA seq dataset for the same type of tissue from mice but there are…

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Sex specific molecular networks and key drivers of Alzheimer’s disease | Molecular Neurodegeneration

Differential gene expression profiles of female and male AD versus control The numbers of differentially expressed genes (DEGs) identified from different comparisons (AD versus normal aging control subjects; females versus males) were shown in Fig. 1A and Supplemental Fig. 1A. In the PHG region, DEG signatures generated from three comparison groups…

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Translational Bioinformatics Scientist – (Office or Remote) – New York

Description Translational Bioinformatics Scientist Arcus is seeking a Bioinformatics Scientist that will work in a highly embedded, collaborative model with colleagues across the organization. Position title would be commensurate with years of relevant experience. The scientist will be expected to work effectively on highly technical interdisciplinary teams and be driven…

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MULTI-seq Sample Multiplexing for Single Cell Analysis and Sequencing

Single-cell RNA-seq (scRNA-Seq) is a powerful but relatively low-throughput tool to analyze gene expression at the single-cell level. Discover our new MULTI-seq system, developed to multiplex sample types using lipid-modified oligonucleotides (LMOs) complexed with unique DNA sample barcodes, allowing for multiple samples to be pooled together in the same single-cell…

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Research Associate in Bioinformatics – London

Job description Job summary We are seeking to recruit a Research Associate in the field of bioinformatics to work in a world-leading research group at the intersection of molecular biology and insect vector control. You will join the laboratory of Professor Andrea Crisanti based at the South Kensington Campus. Our…

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Research Associate in Bioinformatics at Imperial College London

Location: South Kensington Campus  Job Summary  We are seeking to recruit a Research Associate in the field of bioinformatics to work in a world-leading research group at the intersection of molecular biology and insect vector control. You will join the laboratory of Professor Andrea Crisanti at the South Kensington Campus….

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How to create a Seurat object from the `xxx_metadata.txt.gz ` and `xxx_counts.txt.gz` files?

How to create a Seurat object from the `xxx_metadata.txt.gz ` and `xxx_counts.txt.gz` files? 0 Dear all, I downloaded two files of scRNA-seq data from GEO, including xxx_metadata.txt.gz and xxx_counts.txt.gz files. I want to load these files and create a Seurat object. The xxx_metadata.txt.gz file can be read by: metadata <-…

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Voyager Therapeutics hiring Bioinformatics Engineer (Capsid Discovery) in Cambridge, MA, US

About Voyager Therapeutics Voyager Therapeutics is a gene therapy company developing life-changing treatments for fatal and debilitating diseases of the central nervous system (CNS). Voyager is committed to advancing the field of AAV (adeno-associated virus) gene therapy through innovation and investment in vector optimization and engineering, dosing techniques, as well…

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Uploading 10x Data into R for Monocle 3

Uploading 10x Data into R for Monocle 3 1 Hi, I am having trouble loading the cell ranger data into R. I am a beginner, so please excuse my lack of knowledge of R and other terminology. Here is what shows up on my script. cds <- load_cellranger_data(“C:/Users/myname/Downloads/10x_data”) Error in…

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How to use Cyclone to predict cell cycle from single cell Multiomic data (scRNA part)

How to use Cyclone to predict cell cycle from single cell Multiomic data (scRNA part) 0 This is the code I am using to predict cell cycle phases. But I keep getting NA from the final output. I am using Gene Expression part from the single cell multiomic data that…

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MGI Tech, Xpress Genomics partner on sequencing technologies

MGI Tech, a Shenzhen, China-based firm focused on the development and distribution of sequencing instruments and reagents, on Wednesday announced that it had signed a licensing agreement with Xpress Genomics. The agreement is aimed at developing scalable solutions that combine Xpress Genomics’ deep single-cell RNA sequencing (scRNA-seq) expertise with MGI’s…

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Five Applications of Single-Cell Analysis Technologies

Single-cell analysis methods are accelerating research in a range of areas, including immunology, cancer and neuroscience. In this listicle, we explore some of the methods being used and how they are enabling interrogation of complex biology in unprecedented detail. Download this listicle to discover recent examples of how single-cell analysis…

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Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain

Analysis overview This manuscript reports the collective efforts from the teams that participated in the SpaceJam Hackathon (spacetx.github.io/spacejam.html) organized by the SpaceTx Consortium. We explored multiple approaches to assign the spatial data with reference scRNA-seq cell type annotations and developed meta-analysis strategies to combine the cell type assignment results from…

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Why FindMarkers between conditions shows pct.1 and pct.2 as 1 for most of the genes?

Why FindMarkers between conditions shows pct.1 and pct.2 as 1 for most of the genes? 1 I have a Seurat object data which has identified seurat_clusters. And there are two conditions treatment and notreatment for this dataset. I performed DEA between conditions in a specific cluster 3 using the FindMarkers…

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Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap

Sample preparation Arabidopsis thaliana accession Col-0 seeds (hereafter Arabidopsis) were sown on square plates containing Linsmaier and Skoog medium (Caisson Labs, catalogue no. LSP03) with 0.8% sucrose solidified with 1% agar (Caisson Labs, catalogue no. A038). Plates were kept vertically for 5 days in a growth chamber under an 8:16 h light/dark…

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Genome-wide association study of thoracic aortic aneurysm and dissection in the Million Veteran Program

Common variants associated with TAAD We designed a two-phased GWAS. The initial MVP discovery analysis was composed of 8,626 individuals (7,050 European, 1,266 African and 310 Hispanic ancestry participants) with TAAD and 453,043 disease-free individuals from the same ancestral groups (Supplementary Fig. 1); their baseline characteristics are presented in Supplementary…

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Speed of Cell-Cell interaction analysis on scRNA-seq data

Speed of Cell-Cell interaction analysis on scRNA-seq data 0 Hi all, i am trying to perform Cell-Cell interaction analysis on scRNA-seq data processed by Seurat. And I’m using Cellchat for analysis package, but it is taking forever, I have about 10k cells in each samples. and total sample numbers are…

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Transposons contribute to the acquisition of cell type-specific cis-elements in the brain

De novo motifs with high variability in chromatin accessibility across cells are similar to known binding motifs of neural differentiation-related transcription factors To discover accessible DNA motifs that are important for cell-type specificity in the mouse adult prefrontal cortex (P56), we first investigated whether cell types are characterized by k-mer…

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data.signaling matrix error when using mouse database (Error in identifyOverExpressedGenes)

Cellchat error: data.signaling matrix error when using mouse database (Error in identifyOverExpressedGenes) 0 Hi, I’m having an error similar to this cellchat user (github.com/sqjin/CellChat/issues/264). If I run CellChatDB.mouse, and I subset my cellchat object (subsetData), I get this error: Error in identifyOverExpressedGenes(cellchat_DMSO) : Please check `object@data.signaling` and ensure that you…

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The University of British Columbia hiring Bioinformatician in Greater Vancouver Metropolitan Area

Staff – Non Union Job Category M&P – AAPS Job Profile AAPS Salaried – Statistical Analysis, Level B Job Title Bioinformatician Department LSI Bioinformatics Facility | Life Sciences Institute | Faculty of Science Compensation Range $6,677.33 – $10,433.50 CAD Monthly The Compensation Range is the span between the minimum and…

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City of Hope hiring Staff Scientist – Translational Bioinformatics in Duarte, California, United States

About City Of HopeCity of Hope’s mission is to deliver the cures of tomorrow to the people who need them today. Founded in 1913, City of Hope has grown into one of the largest cancer research and treatment organizations in the U.S. and one of the leading research centers for…

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Staff Scientist – Translational Bioinformatics job with City of Hope

About City of Hope City of Hope’s mission is to deliver the cures of tomorrow to the people who need them today. Founded in 1913, City of Hope has grown into one of the largest cancer research and treatment organizations in the U.S. and one of the leading research centers…

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Team identifies IL-17 protein as key factor in skin aging

Dermal cell characterization by 10X scRNA-seq. a, Workflow used to obtain dermal cells of adult and aged mouse back skin. Single-cell suspensions were enriched separately for EpCAM–CD45– and CD45+ cells by FACS. Transcriptomes of sorted single cells were then analyzed by 10X scRNA-seq. For CD45+ cells, n = 7 mice for the adult…

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Tox4 regulates transcriptional elongation and reinitiation during murine T cell development

Pan-hematopoietic Tox4 deletion reduces number of multipotential progenitors and impairs T cell development To understand the role of TOX4 in development, we generated Tox4 conditional knockout mice by the CRISPR-Cas9 methodology, and two loxP sites in the same orientation were inserted upstream and downstream of exons 4–6, respectively (Supplementary Fig. 1a). Considering…

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SENIOR RESEARCH SPECIALIST job with University of Missouri – Columbia

Hiring Department Dalton Cardiovascular Research Center Job Description Provides technique support of the cardiovascular research program. Requires advanced expertise in molecular and cellular biology, and bioinformatics analysis in the cardiovascular system. Techniques required include, but not limited to primary cultures of cardiovascular cells, genetical manipulation in vitro such as gene…

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Postdoctoral Associate- Bioinformatics/Cancer Genomics

Summary The Cheng Lab at Baylor College of Medicine is searching for highly motivated and talented post-doc candidates to work on Bioinformatics and Computational Biology in Cancer Genomics and Immunology. The position will be involved in the development and/or application of computational approaches to understand the mechanism of cancer…

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CellRanger problem

Hey, what’s up? I’m using the CellRanger for scRNA and this problem appears: Generating STAR genome index (may take over 8 core hours for a 3Gb genome)… Jun 07 19:02:11 ….. started STAR run Jun 07 19:02:11 … starting to generate Genome files Jun 07 19:02:11 … starting to sort…

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P-value histogram of testLinearModel is not uniform

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…

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Cracking cancer: Using long-read RNA sequencing for cancer neoantigen discovery

When developing effective personalized immunotherapies, such as cancer vaccines, a pivotal factor lies in uncovering tumor neoantigens that can serve as crucial therapeutic targets. Traditionally, neoantigen discovery heavily relied on short-read sequencing technology, with a predominant focus on neoantigens resulting from single-nucleotide variants (SNVs). However, recent advancements have unveiled the…

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Bioconductor – CHETAH

DOI: 10.18129/B9.bioc.CHETAH     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see CHETAH. Fast and accurate scRNA-seq cell type identification Bioconductor version: 3.13 CHETAH (CHaracterization of cEll Types Aided by Hierarchical classification) is an accurate, selective and fast scRNA-seq classifier. Classification is guided…

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retaining only the clusters of interest

retaining only the clusters of interest 0 Hey I am trying to subset only the clusters of my interest by the following command diff2 <- subset(merged_seurat_filtered, idents = c(0:16),) There are 21 clusters in total and I want to omit the last 4 clusters from my Seurat object, but when…

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Bioconductor – peco

DOI: 10.18129/B9.bioc.peco     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see peco. A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data Bioconductor version: 3.13 Our approach provides a way to assign continuous cell cycle phase using scRNA-seq data, and consequently,…

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Open PhD position in Bioinformatics

München   The Beltrán and Kerschensteiner Labs at the Biomedical Center of the Ludwig-Maximilians University Munich are looking for a PhD student in Bioinformatics. The candidate will develop bioinformatic methods for integrative analysis of scRNA-seq and snRNA-seq datasets from multiple sclerosis (MS) human samples and related MS models. Such integrative…

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Element Enters the European Genomics Market with New Customers and a Growing Team

SAN DIEGO and AMSTERDAM, June 5, 2023 /PRNewswire/ — Element Biosciences, Inc., the developer of the Element AVITI™ System, an innovative DNA sequencing platform disrupting genomics, is pleased to announce that the AVITI is now available in Europe, in addition to Asia and the Middle East. VIB, Flanders’ leading life…

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How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by cell barcode?

How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by cell barcode? 1 Hello everyone, I have a sample of scRNA seq data (A.Thaliana) generated by 10X Genomics. The data is composed of R1 (cell barcodes and UMIs) and R2 (actual reads)…

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Bioinformatics in Next Generation Sequencing (BiNGS) – Icahn School of Medicine hiring Junior Bioinformatician in New York, New York, United States

Junior Bioinformatician position in BiNGS   We are seeking a junior bioinformatician for the Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) core, to lead transcriptomics and epigenetics data analysis projects related but not limited to cancer biology, skin biology, developmental biology, diabetes, and neuron biology.   The mission…

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Quantification and statistical modeling of droplet-based single-nucleus RNA-sequencing data

doi: 10.1093/biostatistics/kxad010. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205, USA. 2 Department of Genetic Medicine, Johns Hopkins School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA. Item in Clipboard Albert Kuo et…

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Transfer learning enables predictions in network biology

Vaswani, A. et al. Attention is all you need. Preprint at doi.org/10.48550/arXiv.1706.03762 (2017). Devlin, J., Chang, M. W., Lee, K. & Toutanova, K. BERT: pre-training of deep bidirectional transformers for language understanding. In Proc. 2019 Conference North American Chapter of the Association for Computational Linguistics: Human Language Technologies Vol. 1…

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Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing | BMC Cancer

Single-cell and single-nucleus RNA sequencing of sarcoma subtypes In this work, we studied sarcomas from varying tissue origins, including osteosarcoma (OS), Ewing sarcoma (ES), and desmoplastic small round cell tumor (DSRCT) (Fig. 1). We used different dissociation protocols: Miltenyi Tumor Dissociation Kit, cold-active protease derived from Bacillus licheniformis, and Nuclei EZ…

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Cell type sub-clustering across multiple samples in scRNA-seq

Cell type sub-clustering across multiple samples in scRNA-seq 0 Hi, This still might be controversial and also project-specific question, but under what circumstances one should or should not apply integration/batch effect correction when focusing on one specific cell type from different samples? Note that the integration and clustering for all…

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Query qbout single cell sequencing

Query qbout single cell sequencing 0 I am a new student working with scRNA seq data regarding which i have a few queries. can single cell rna-sequencing both single end or paired end ? If paired end then what information is in _1 and _2 fastq files because i have…

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University of Pittsburgh School of Medicine hiring Postdoc associate in bioinformatics in Pittsburgh, Pennsylvania, United States

Post Doctoral Associate in biostatistics and bioinformatics for liver research Genomics and Systems Biology Core Pittsburgh Liver Research Center Pittsburgh Liver Research Center (PLRC, livercenter.pitt.edu/) is currently accepting applicants. Specifically, this position will focus on the field of biostatistics and bioinformatics analysis of genomic data, supervised by Dr. Silvia Liu…

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ScRNA data

ScRNA data 1 I have a single cell paired end data 140 bp long, contain 140 bp in both files _1 and _2 with no barcode and UMI information. How can i extract the barcodes and UMIs to use as an input for starsolo tool for alignment from the paired…

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Research Assistant in Bioinformatics job with KINGS COLLEGE LONDON

Job description An exciting opportunity has arisen to work on a project investigating the molecular pathogenesis of palmoplantar pustulosis, a severe and disabling skin disorder that is notoriously difficult to treat. The study, which is led by Profs. Francesca Capon and Catherine Smith, will seek to identify new disease genes…

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Research Assistant in Bioinformatics job with KING’S COLLEGE LONDON

Job description An exciting opportunity has arisen to work on a project investigating the molecular pathogenesis of palmoplantar pustulosis, a severe and disabling skin disorder that is notoriously difficult to treat. The study, which is led by Profs. Francesca Capon and Catherine Smith, will seek to identify new disease genes…

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How to generate cDNA file from genome FASTA and GTF?

How to generate cDNA file from genome FASTA and GTF? 1 Hello! I am new to single-cell RNASeq and am currently trying to run Kallisto | bustools to make a pseudoalignment. The organism that I work with, Ciona intestinalis is not a model organism, so the files on Ensembl are…

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Single-cell gene and isoform expression analysis reveals signatures of ageing in haematopoietic stem and progenitor cells

Annotation of short-read scRNA-seq data with isoform-level information Using fluorescence-activated cell sorting (FACS), we isolated the Lineage-negative, cKit (Cd117) positive (LK) cell fraction of mouse bone marrow cells, a population containing stem and progenitor cells14 from young (8 weeks old, n = 3) and aged (72+ weeks old, n = 3) mice. We generated…

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Analytical criteria to say a transcript is expressed in single-cell

Analytical criteria to say a transcript is expressed in single-cell 1 Hello! I’ve been working and analyzing single-cell RNAseq datasets recently. When I reach the point of normalized counts matrices for different cell types (after filtering for doublets) I face a question that I can’t answer: What is a good…

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CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones.

Abstract Motivation:Single-cell RNA-sequencing (scRNA-seq) has enabled studies of tissue composition at unprecedented resolution. However, the application of scRNA-seq to clinical cancer samples has been limited, partly due to a lack of scRNA-seq algorithms that integrate genomic mutation data. Results:To address this, we present. CONICS:COpy-Number analysis In single-Cell RNA-Sequencing. CONICS is…

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Co-Expression of All Genes with a Single Gene (Spatial Transcriptomics)

Co-Expression of All Genes with a Single Gene (Spatial Transcriptomics) 0 Hi all, I am struggle to figure out a solution to a (seemingly) simple. Using Seurat, I would like to find which genes are most highly expressed with individual marker genes spatial transcriptomic dataset. I have an integrated dataset…

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Senior Data Scientist for Cancer Pharmacogenomics job with Human Technopole

APPLICATION CLOSING DATE: July 3rd, 2023 Human Technopole (HT) is a new interdisciplinary life science research institute, created and supported by the Italian Government, with the aim of developing innovative strategies to improve human health. HT is composed of five Centers: Computational Biology, Structural Biology, Genomics, Neurogenomics and Health Data Science….

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Advisor/Sr. Advisor – Bioinformatics job with Eli Lilly and Company

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our 35,000 employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of…

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Associate Data Scientist – Genetics (NGS) job with University of Texas MD Anderson Cancer Center

SUMMARY The Genetics Department is a basic science department located in the George and Cynthia Mitchell Basic Sciences Research Building at the world-renowned University of Texas MD Anderson Cancer Center in the heart of the Texas Medical Center. The focus is on advancing knowledge of the molecular genetic mechanisms that…

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Rutgers University hiring Informatics Specialist (Bioinformatics) in Newark, New Jersey, United States

Below you will find the details for the position including any supplementary documentation and questions you should review before applying for the opening. To apply for the position, please click the Apply for this Job link/button.If you would like to bookmark this position for later review, click on the Bookmark…

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Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress

Hagemann-Jensen, Ziegenhain, Sandberg (2022) Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress Nat Biotechnol (IF: 68.2) Abstract Current single-cell RNA sequencing (scRNA-seq) methods with high cellular throughputs sacrifice full-transcript coverage and often sensitivity. Here we describe Smart-seq3xpress, which miniaturizes and streamlines the Smart-seq3 protocol to substantially reduce reagent use…

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Bioinformatics Scientist – Carlsbad, CA

Position Title: Bioinformatician Scientist Classification: Exempt Reports To: TBD Who is Active Motif? Active Motif is the industry leader in developing and delivering innovative tools to enable epigenetics and gene regulation research. We are committed to providing the highest quality products and superior service & support to serve the life…

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Linking Expression of Cell-Surface Receptors with Transcription Factors by Computational Analysis of Paired Single-Cell Proteomes and Transcriptomes

Complex signaling and transcriptional programs control the development and physiology of specialized cell types. Genetic perturbations in these programs cause human cancers to arise from a diverse set of specialized cell types and developmental states. Understanding these complex systems and their potential to drive cancer is critical for the development…

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Amazon Omics Beefs up Managed Services with Pre-Built Workflows, GPU Support

BOSTON – Amazon Web Services this week introduced new features for its nascent Amazon Omics service, including a collection of “pre-built” workflows, support for graphical processing units (GPUs), direct data uploads through an application programming interface (API), and streamlined variant querying and analysis. AWS launched Amazon Omics last November. The…

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How to analyze mars-seq single end-read scRNAseq data?

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…

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an extremely low rate of correct barcodes was observed

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…

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