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Tag: CITEseq
Bioinformatics Software Engineer Consultant Job at ProCogia
ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…
ProCogia hiring Bioinformatics Software Engineer Consultant in Vancouver, British Columbia, Canada
ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…
CITE-seq data visualization
Hello, I have produced quite some single cell CITE-seq data at the single cell level, using the 10x genomics platform and analyzed in Seurat. I am at the moment trying to visualize the protein markers from the CITEseq against to each other in a way that would resemble how we…
Frederick National Laboratory Bioinformatics Analyst II/III in Bethesda, MD | 862626552
Bioinformatics Analyst II/III Job ID: req3719Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….
merge vdj data in citeseq seurat onject
merge vdj data in citeseq seurat onject 0 I want to merge vdj-t data with citeseq seurat object, i tried, it gave me this error Error in as.character.default(new(“Seurat”, assays = list(RNA = new(“Assay”, : no method for coercing this S4 class to a vector Seurat • 369 views • link…
Platelet factors attenuate inflammation and rescue cognition in ageing
Animal models The C57BL/6 mouse line was used for all of the experiments (The Jackson Laboratory and National Institutes of Aging). Homozygous Pf4-KO mice were previously generated and characterized as described48. Pf4-KO mice were a gift from M. Anna Kowalska. Heterozygous mice were bred to generate Pf4-KO and WT littermate…
counts of cite-seq-count vs. cellrenager varies tremendously
I was wondering if I can still use (trust?) the cite-seq-count tools. The tool was not updated for a few years and I’m not sure, if it is still on the level of for example cellranger. I have tested the 5k_pbmc_protein_v3_nextgem data set from 10x Genomics with CITE-Seq data for…
Help concatenating var for cite seq – scanpy
I have a CITE seq experiment where the GEX and antibody capture were mapped separately, so that I have to load in two different matrices. adata_adt = sc.read_10x_mtx( “data/CITESeq_381/”, gex_only = False ) adata_gex = sc.read_10x_mtx( “data/GEX_381/filtered_feature_bc_matrix/”, gex_only = True ) I subset to only cells with GEX and ADT…
single cell multi-modal data (CITEseq) batch correction
single cell multi-modal data (CITEseq) batch correction 0 I’m working with a BD Rhabsody AbSeq data set containting a targeted scRNA and surfce protein (ADT) layer measured in two batches. In general I aim to integrate both modalities (e.g. MOFA+ or SeuratV4) for a joined analysis. While I perform QC…
Running TOTALVI data in which subset of cells do not have citeseq data – scvi-tools
Here is the error message from before ValueError Traceback (most recent call last) <ipython-input-29-3de112adfeee> in <module> —-> 1 vae5.train() /opt/conda/lib/python3.8/site-packages/scvi/model/_totalvi.py in train(self, max_epochs, lr, use_gpu, train_size, validation_size, batch_size, early_stopping, check_val_every_n_epoch, reduce_lr_on_plateau, n_steps_kl_warmup, n_epochs_kl_warmup, adversarial_classifier, plan_kwargs, **kwargs) 257 **kwargs, 258 ) –> 259 return runner() 260 261 @torch.no_grad() /opt/conda/lib/python3.8/site-packages/scvi/train/_trainrunner.py in __call__(self)…
using CITE-seq data to cluster single cells
using CITE-seq data to cluster single cells 0 Hello, I am trying to cluster single cells using the ADT reads from the CITEseq (generated with the 10x platform). Ideally, I would like to use the information from two ADT features. I have tried the kmeans function on a count matrix…
Cell Type Prediction – covering 45 immune cell types
Tool:Cell Type Prediction – covering 45 immune cell types 0 Dear Colleagues, We just released a new tool for predicting cell types from single-cell RNA-seq data (and scRNA-seq + CITE-Seq). Currently, it covers 45 sub-types of immune cells. More subtypes are continuously being added. This tool is available in both…
Corelate TCR data to clusters/GEX/CITEseq data
Corelate TCR data to clusters/GEX/CITEseq data 1 Hello everyone, I just added my TCR VDJ data as metadata to my Seurat object (as described in the tutorial here). So, I basically ended up with two different collumns of metadata where my barcodes are assigned to the clonotypes and the cdr3…