Tag: scATAC-SEQ

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…

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…

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…

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

Too many differential peaks derived from FindMarkers() [Signac] 0 I am currently conducting scATAC-seq downstream analysis and just ran FindMarkers() comparing two biological conditions. In all, the number of diff. peaks turned out as ~5,000 which is rather high (the expected is around 500). How would I go about this?…

NEW YORK – The Allen Institute for Immunology is looking to commercialize a multiomic gene panel to screen for immune disorders based on an internally developed bioinformatics platform for analyzing longitudinal single-cell RNA sequencing data. In doing so, the Seattle-based research institute hopes to make scRNA-seq more accessible as a…

scATAC integration 0 I am integrating 5 different datasets for a scATAC-seq analysis. I have had the following error persist for weeks; have looked online as well for possible solutions yet nothing has worked. Has anyone run into this issue? The following code is: object.list = list(sample1,sample2, sample3, sample4, sample5)…

How to aggregate scATAC and multiome scATAC data while preserving the barcodes from the multiome 0 Hello everyone, I am working on single-cell analysis of my data. From 10X Genomics, I have scATAC-seq data and also multiome (measurements of scRNA + scATAC from the same cell). After using Cell Ranger…

ATAC Integration Help 0 Pretty much desperate at this point since I’ve had this error for a week. The output is the following after entering the following command: integration.anchors<- FindIntegrationAnchors( object.list = list(Seurat_1, Seurat_2, Seurat_3), anchor.features = row.names(Seurat_1), assay = c(‘peaks’, ‘peaks’, ‘peaks’), k.filter = NA, reduction = “rlsi”, dims…

  The Big Data in BioMedicine Group at the Chair of Experimental Bioinformatics (School of Life Sciences, Technical University of Munich (TUM)) invites applications for a postdoctoral position for the development of innovative algorithms for the joint analysis of single-cell & spatial transcriptomic data in the framework of the Novo…

PostDoc Position – Innovative Computational Methods: The Big Data in BioMedicine Group at the Chair of Experimental Bioinformatics (School of Life Sciences, Technical University of Munich (TUM)) is seeking a Postdoctoral Researcher to develop innovative algorithms for the joint analysis of single-cell & spatial transcriptomic data in the framework of…

MACS to Signac 1 Hey guys– Once MACS is completed running, how would I feed the peaks/bed file into Signac for each sample up to merging and finally clustering? I believe the vignette only demonstrates if one were to add *fragment files and I need the peaks file from MACS…

MACS Error 1 I’m currently running MACS2 and have the following error: $ macs2 callpeak -f BAMPE -t READS.bed -g hs -n test -B -q 0.01 . . . . **(MACS2/IO/Parser.c:12841)struct.error: unpack requires a string argument of length 4** Any suggestions? I’ve run and re-run this to no avail. scatac-seq…

CellOverview of the Oracle algorithm The CellOracle workflow is made up of several steps. We Tested and implemented CellOracle Python Versions 3.6 and 3.8 were developed and made available for use in the Jupyter Notepad environment CellOracle code can be downloaded open-source on GitHub.github.com/morris-lab/CellOracle), along with detailed descriptions of functions…

The Position The Piskol lab in Genentech’s Research and Early Development organization is looking for an exceptional Postdoctoral Fellow who will pair state-of-the-art single cell assays with computational methods to study the intra-tumoral heterogeneity of metastatic colorectal cancer and the collaborative role of oncogenic signaling pathways in cancer maintenance, progression…

scATAC-seq workflow 0 Help. I am still new to the concept of scATAC-seq and was wondering if anyone could provide a straightforward workflow. I am referring to the Signac vignettes but it seems to go back and forth between tutorials. I am starting out with 2 samples– one knockout and…

scATAC merging of files 0 Bit of a simple question, however when you are given 2 different treatments of a condition– say Wildtype and the other being a knockout of some sort, would you go through an entire analysis for the wild type and separately another analysis for the knockout;…

CoveragePlot in Signac from MACS2 Object 0 I am currently trying to produce a CoveragePlot() to locate a number of transcription factors; however instead of the input being a Chromatin Assay or Seurat Object, I wanted to pass output files passed by MACS2 which was run in the terminal. I…

Having a lot of trouble converting Gene Ranges to GeneID. 0 I’m having trouble converting gene ranges to gene ids for mm10. For example I have a dataframe of “chromosome”, “start”, “end”, and I want the associated “GENE SYMBOL” for each row. I was looking online, which brought me to…

linkedin.com Apply on Website The British Dental Journal Bioinformatics Research Scientist to develop and apply innovative analytical approaches to study the mechanisms of normal hematopoiesis and blood diso… Role: Research Scientist, Category: Scientific, Size: 1-10 Sr Bioinformatics Research Scientist: The British Dental Journal Bioinformatics Research Scientist to develop and apply…

We are looking for a Bioinformatics Analyst I. The position will involve analysis and visualization of large throughput multi-omics molecular profiles in various human disease models. Data types include single cell transcriptomics, proteomics, metabolomics and epigenomics analysis (MS proteomics and phosphoproteomics, scRNA-Seq, scATAC-Seq, scWGBS-Seq, scCut&Tag), and bulk tissue datasets spanning…

At Bristol Myers Squibb, we are inspired by a single vision – transforming patients’ lives through science. In oncology, hematology, immunology and cardiovascular disease – and one of the most diverse and promising pipelines in the industry – each of our passionate colleagues contribute to innovations that drive meaningful change….

Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…

Hi all, I am new to R and Seurat, and I am following Seurat tutorials to find anchors between RNA-seq and ATAC-seq data according to: Combining the two tutorials is difficult for a cell line data set I am using for SNARE-seq Human here. I managed to run the following…

Does anyone know of any public scATAC-seq databases? Up until now I’ve been using the scATAC.Explorer library in R to get my scATAC datasets, but there doesn’t seem to be a fragment file associated with any of the experiments. I’d like to plot some gene activity matrices/coverage plots. Alternatively, if…

Job description A Postdoctoral Research Associate (PDRA) – Computational biology position is available in the Centre for Gene Therapy and Regenerative Medicine, King’s College London. This is an exciting opportunity to join an interdisciplinary team of scientists working on a Wellcome Trust funded research programme aimed at studying the mammalian…

Reviewer #1 (Public Review): Droplet-based single-cell method development has stalled in the past years. The field has been overtaken by commercial solutions that optimized performance, but at much higher costs and without any possibility for customization. More recently, combinatorial indexing methods (e.g. SPLIT-seq) have gained popularity, requiring no specialized equipment…

Postdoctoral position in bioinformatics – focused on single-cell immune transcriptomics Login and apply Do you want to contribute to improving human health? We are looking for an ambitious postdoctoral fellow with solid genome-wide bioinformatics and computational biology skills to join our highly accomplished team. We offer a stimulating environment in…

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….

Arokiaraj, Cynthia Mary (2022) Cellular and Molecular Atlas of the Macaque Dorsal Horn. Doctoral Dissertation, University of Pittsburgh. (Unpublished) Abstract The spinal cord dorsal horn occupies a key position in the central nervous system, as it is the first site of integration of somatosensory input from the periphery. Local interneurons…

tSNE and UMAP of scATAC-seq data looks like spaghetti 0 I would like to use R to generate cluster my 20k cells from a single cell ATAC-seq experiment. I ran PCA then selected the first 50 components, which were put into tSNE’s normalize_input() then Rtsne(). This is the result I…

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:…

How to interpret Nucleosome banding pattern in scATAC-Seq? 0 Hello, I am following Signac vignette to perform QC on my single cell ATAC-Seq data. As per my understanding the vignette considers all cells with nucleosome signal > 4 to have a high nucleosomal signal strength and nucleosome signal is calculated…

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…

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…

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…

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…

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…

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…

Low mapping rate of 10X scATAC-seq reads 0 Hey Guys, I’m working on a scATAC-seq project using 10X technologies. My samples including several different species. the problem is that for one species (2 sample in total), both of the mapping rate of reads from these 2 samples are very low…

– 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…

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…

How to merge Bulk ATAC-SEQ with scATAC-SEQ result? 0 Hello, I am using Signac for analyzing scATAC-SEQ for this experiment, we also have some Bulk ATAC-seq data. How can I show the bulk ATAC data as an extra track on Signac browser ? Or Can I merge scATAC-SEQ peak region…

How to generate feature Data(fData) 0 I’m trying to analyze scATAC-seq data using Cicero, but I lack the metadata for peak(fData). I don’t know how to generate this metadata.Can someone tell me which tool can produce it? Note: This data was not generated using the 10X platform but Fluidigm C1….

Sequencing file conversion 0 Hi, friends, I downloaded a set of scATAC-seq BAM files from an article database, and the author said that a BAM file is information about a cell. However, after a few days’ analysis of the script given by the author, I found that a CSV file…