Tag: Seurat

Merging multiple samples in Seurat

Hello! I am very recent to snRNAseq , however has recently started using Seurat to process the data I have available. This is more of a clarification that I have understood the tutorials appropriately. A breakdown of my data: I have snRNAseq data from diseased with mutation, diseased without mutation…

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Update to (git-version 2.0.1 revision commit).

* gnu/packages/bioinformatics.scm (r-sccustomize): Update to (git-version 2.0.1 revision commit). Change-Id: I4e4b499a658eaed0396263d1d9fd277a541a13d9 — gnu/packages/bioinformatics.scm | 87 ++++++++++++++++—————– 1 file changed, 43 insertions(+), 44 deletions(-) Toggle diff (108 lines) diff –git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2546454acd..3e7b99ee61 100644 — a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10245,55 +10245,54 @@ (define-public r-presto (license license:gpl3)))) (define-public r-sccustomize – (let…

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scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts?

scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts? 1 @03836aaf Last seen 5 hours ago United States Hi, I’m using AggregateExpression() function to convert my scRNA-seq data into pseudobulk for differential expression with Deseq2. I’m wondering whether AggregateExpression() simply sums the counts for each gene in each cell, or…

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Single-cell RNA-seq workflow

In this tutorial we walk through a typical single-cell RNA-seq analysis using Bioconductor packages. We will try to cover data from different protocols, but some of the EDA/QC steps will be focused on the 10X Genomics Chromium protocol. We start from the output of the Cell Ranger preprocessing software. This…

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Bioconductor T2T-CHM13

Comment: Reduce single cell experiment size to use as reference for annotation with Singl by elgomez • 0 Thank you, James! I ended up running seurat FindVariableFeatures with nfeatures = 10000 and then subsetting the object to just those varia… Comment: Help with model.matrix and creating the right contrast matrix…

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Single Cell Data Scientist at European Molecular Biology Laboratory (EMBL)

About the team/job We are looking for a Bioinformatician to join the Open Targets data team. We are seeking an enthusiastic team member to expand our informatics platforms through the integration of single cell omics data to enhance drug discovery. This role would suit someone with experience in data integration…

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Bioinformatics Jobs for December 2023

Bioinformatics is an ever-evolving field of science that uses computing and statistical techniques to analyze and interpret biological data, such as DNA and protein sequences, gene expression levels, and metabolic pathways. With the help of a Bioinformatics Developer, you can solve complex problems associated with biomedicine, biotechnology, drug discovery and…

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Confusing results from FindConservedMarkers in Seurat

Confusing results from FindConservedMarkers in Seurat 1 I am trying to identify marker genes from clusters identified by running Seurat. I use FindConservedMarkers for this as I have multiple conditions in my dataset and I use grouping.var as my multiple conditions. However, when I look at the top 5 marker…

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How to remove center population from seurat cluster

How to remove center population from seurat cluster 0 Dear all, apologize for many posts. I have done my clustering, but there is weird tidy population (in red circle) that is not stay close to its assigned cluster (kindly see attach). In the attached imaged, that cluster has been assigned…

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Postdoctoral Research Fellow, Computational Biology / Bioinformatics @ Visterra

Summary Visterra is seeking a highly talented, self-motivated and innovative Postdoctoral Research Fellow to join our Technology Platform team. The fellow will lead the conceptualization and implementation of advanced machine learning approaches to large single cell, spatial and multi-omic datasets. The role will involve developing creative approaches to leverage machine…

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How can i control the cluster number in scRNASeq clustering by Seurat package

How can i control the cluster number in scRNASeq clustering by Seurat package 2 Hi all, I analysised the 10x dataset by Seurat pkg, when i used the TSNEPlot function to plot the TSNE plot of clustering result, i found the number of cluster always different. How can i control…

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Tutorials for Spatial Transcriptomics

Tutorials for Spatial Transcriptomics 0 Hi all! I am a PhD student, I am familiar with single-cell transcriptomics, my PI is interested in me learning about spatial transcriptomics. I have searched for couple of tutorials, however they are not that detailed. I request you all to kindly send me few…

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JoinLayers function for Seurat Object for annotation with SingleR

Dear all, I have the following issue: I have a Seurat object with 7 layers of raw gene expression counts for 7 different patients. In order to annotate the object with SingleR I have now used the function “JoinLayers” to combine all counts into one layer of counts of all…

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Finding differentially expressed genes between Seurat clusters

Good afternoon, I am working with a dataset of 7 patients. I have merged all raw counts to one count object with JoinLayers: Now I would like to know whether there are certain genes differentially expressed between my Seurat clusters. For that I ran markers_all<-FindAllMarkers(kid.filtered_new, test.use=”DESeq2″, slot=”counts”) However, it does…

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Bioconductor Code: CelliD

# CelliD v0.99 R package for gene signature extraction and cell identity recognition at individual cell level from single-cell RNA-seq. ![logo](https://github.com/RausellLab/CelliD/blob/gh-pages/tools/sticker.png?raw=true) —————————————- Welcome to the official Github repository of the **CelliD** software presented in the Article [Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID, Nature…

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Can’t do runPCA after merging a splited Seurat object before UMAP

Hi everyone, When I started my analysis, I merged 3 samples. merged_seurat <- merge(x = PC9_1_raw_feature_bc_matrix, y = c(PC9_2_raw_feature_bc_matrix, PC9_3_raw_feature_bc_matrix), add.cell.id = c(“PC9_1”, “PC9_2”, “PC9_3”)) After cell filtering, I checked the cell cycle and batch effects (no batch effect, I won’t do integration). I split my Seurat object to do…

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scRNA data analysis , how to compare pattern in multiple samples

Hello Everyone . I am new to single cell data . in this path G:\RNA\sc\scdata I have 3 files Sample5D_barcodes Sample5D_features Sample5D_matrix.mtx I want to see cell clusters and differentially expressed genes for this single cell sample. I am running this command in R install.packages(c(“Seurat”, “ggplot2”, “Matrix”, “dplyr”)) library(Seurat) library(ggplot2)…

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Study reveals how maternal diabetes affects birth defects at the single-cell level

In a recent study published in Nature Cardiovascular Research, researchers from California used multimodal single-cell analysis in mice to investigate the mechanisms by which maternal diabetes mellitus contributes to congenital abnormalities in the fetus. They found that during embryogenesis, maternal diabetes alters the epigenomic landscape in cardiac and craniofacial progenitors,…

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Ambient RNA removal method that generates whole (integer) counts

Ambient RNA removal method that generates whole (integer) counts 0 I am envisioning a project that requires removal of ambient RNA counts from cell-containing droplets. On the other hand, I will also need to aggregate counts from individual mice into “pseudobulk” profiles, to use as input to between-condition DE analysis…

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Need to PrepSCTfindMarker again after subset if the original object has already been normalized?

Need to PrepSCTfindMarker again after subset if the original object has already been normalized? 0 Hi, I’ve got a seurat object of 2 samples integrated after QC and SCTv2. I then performed clustering and PrepSCTfindMarker followed by findMarker. These all went smoothly. Then I made a subset from 3 clusters,…

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mouse+human cells in 10x scRNA-seq

mouse+human cells in 10x scRNA-seq 1 Hi everyone, I’m analyzing 10x scRNA-seq data generated from xenografts (mouse + human tissues). I have the following workflow to label cells as either mouse or human: Align 10x scRNA-seq data to mouse+human combined genome using cellranger count. Use the file generated by cellranger…

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Should I scale all genes in single cell Seurat?

Apologise for many posts this weeks. I am wondering in seurat, should I scale all genes for downstream analysis or just some features is okay? I am a bit unclear when it comes to scaling…. I have attached the code here. Also, how do I know which genes are noise/confounding…

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Cellcyclescoring did not work in Seurat V5

Cellcyclescoring did not work in Seurat V5 0 Dear All, Not sure anyone has come across issue with cell cycle scoring in seurat recently. data.filt<- NormalizeData(data.filt) #Cell cycle data.filt<- CellCycleScoring(object = data.filt, g2m.features = cc.genes$g2m.genes, s.features = cc.genes$s.genes) Error in `GetAssayData()`: ! GetAssayData doesn’t work for multiple layers in v5…

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Harmony integration PC variance explained

Harmony integration PC variance explained 0 Hi guys, I ran harmony on my seurat obj and then elbow plot to select the number of PCs for downstream analysis. I found that a number of the earlier PCs explain less variance than the subsequent PCs I am not sure how this…

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DoubletFinder for Python?

DoubletFinder for Python? 3 I’m trying to process s single-cell RNA seq data using Scanpy. I usually use Seurat. One of the major difference when using Scanpy is the lack of scDoubletFinder. The recommended alternative is to use scrublet. However, I find a large difference between the result of scrublet…

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Allen Institute for AI (AI2) hiring Head of Bioinformatics at Stealth Life Science Startup in Seattle, WA

About UsWe are an early stage startup using generative AI to fundamentally change life sciences research and accelerate the pace of biomedical discovery. Genomic data are at the heart of most modern molecular studies and tools, from basic research to clinical decision support, but these data are hard to work…

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Are liger or Seurat CCA good strategies for multiple scRNA-seq data integration?

Are liger or Seurat CCA good strategies for multiple scRNA-seq data integration? 1 Hi, I am working on analyzing multiple scRNA-seq dataset from embryonic tissues at progressive stages. I used three recent integration algorithms 1) liger, 2) Seurat CCA and 3) fastMNN. I started with these based on recommendation from…

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Elevated stress response marks deeply quiescent reserve cells of gastric chief cells

Generation of inducible H2b-GFP knock-in mice Generation of inducible H2b-GFP knock-in mice was performed by using CRISPR/Cas943. In brief, a mixture containing a sgRosa26-1 crRNA43 (8.7 ng/μl, Fasmac, Japan), a tracrRNA (14.3 ng/μl, Fasmac, Japan), a single strand oligo donor nucleotide (ssODN) composed of 5′ arm, adenovirus splicing acceptor, SV40 pA, TRE3G…

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Batch effect correction between Bulk RNA-Seq and scRNA-Seq’s clusters

Batch effect correction between Bulk RNA-Seq and scRNA-Seq’s clusters 1 Hello, I need to compare some samples from different bulk RNA-Seq with some clusters of a scRNA-Seq (not whole sample) to find DEGs. We have undifferentiated samples performed by bulk RNA-Seq and fully differentiated samples (mature ones) are 2-3 clusters…

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MAJOR Computational Biology Research Lab

MAJOR Computational Biology Research Lab (MCBRL) uses computer science algorithms to solve biology related problems, bioinformatics software development and develop bioinformatics cloud computing platforms or services for handling and analyzing large-scale biological data.. The workflow of hdWGCNA analysis for Single-cell Spatial Transcriptomics data RNA-seq Schematicsc/nRNA-seq Schematic ” RNA-seq Schematic 空间转录共表达网络分析流程…

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percentage of cells in each cluster- Seurat

percentage of cells in each cluster- Seurat 0 I am still relatively new to bioinformatics analysis…. I was wondering in Seurat could it be possible to find what percentage of cells in each cluster are PC vs IC cells? I would like to get a spreadsheet of this information. Imagine,…

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Upgrading Phage Therapies to Crush Antimicrobial Resistance

By Andy Tay, PhD Overuse of antibiotics has accelerated the emergence of antimicrobial-resistant (AMR) bacterial species. The World Health Organization named antibacterial resistance as a top public health threat to humanity. In 2022, the Antimicrobial Resistance Collaborators reported that AMR bacteria directly caused 1.3 million deaths and was associated with…

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Smart seq3 analysis

Smart seq3 analysis 1 Hi, I am new to data analysis, so please bear that in mind. I can load 10x data into R, and can follow seurat tutorial. But now I need to work with Smart seq3 data, which is in “RawFASTQ” folder. (I guess this is the list…

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Bioconductor – ggsc

DOI: 10.18129/B9.bioc.ggsc   Visualizing Single Cell Data Bioconductor version: Release (3.18) Useful functions to visualize single cell and spatial data. It supports both ‘SingleCellExperiment’ and ‘Seurat’ objects. It also supports visualizing the data using grammar of graphics implemented in ‘ggplot2’. Author: Guangchuang Yu [aut, cre, cph] , Shuangbin Xu [aut]…

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Filter out doublet and Clustering

Dear all, fellows, I used DoubletFinder from Chris github.com/chris-mcginnis-ucsf/DoubletFinder to filter out doublet cells for each sample individually and used standard seurat pipeline to normalize the data as using following functions because I cannot use SCTransform with seurat 5 as DoubletFinder did not upgrade to match with Seurat5 yet. NormalizeData(object…

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Convert Seurat object to anndata

Hi all, I am trying to save my Seurat object to h5ad to use it as Anndata, I did it before using MuDataSeurat, with Seurat_4.3.0.1. `seurat_object = CreateSeuratObject(counts = out, project=”sample_name”) str(seurat_object) 1st str: Formal class ‘Seurat’ [package “SeuratObject”] with 13 slots ..@ assays :List of 1 .. ..$ RNA:Formal…

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The effects of methylphenidate and atomoxetine on Drosophila brain at single-cell resolution and potential drug repurposing for ADHD treatment

Both MPH and ATX increase the locomotor activity of wild-type Drosophila To investigate the cell type-specific molecular mechanisms of ADHD drugs in the brain at single-cell resolution, we conducted behavioral experiments and scRNASEQ in wild-type (WT) adult male Drosophila melanogaster following exposure to MPH, ATX, and control treatment. Here, we…

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keep getting error while trying to convert Seurat object into a H5ad file

keep getting error while trying to convert Seurat object into a H5ad file 2 I am trying to convert rds file (or Seurat object) to h5ad files using the following command in R: library(scater) library(Seurat) library(cowplot) pbmc_ad <- Convert(from = pbmc, to = “anndata”, filename = “results/pbmc3k.h5ad”) in which pbmc…

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smartseq2 RPKM data

Hi! I have smartseq2 RPKM data (already analysed with Seurat pipeline) and I want to do trajectory analysis of my cells. Having RPKM data I wondered whether I can use Monocle 3 or can it just be used with UMI data (10x) ? In Monocle2 it seemed to be possible…

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lentibarcode and single cell

Hi, I use a high-complexity barcoding (lentibarcode) with a single-cell approach (10X). I’m doing my analysis with Seurat. Each 10X cell barcode is associated with a lentibarcode in my meta.data. I found several cells with the same lentibarcode and made a list of lentibarcodes in more than 20 cells (103…

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Options for assigning cell labels to barcodes from CITE-seq experiment

Options for assigning cell labels to barcodes from CITE-seq experiment 0 I have barcodes from a CITE-seq experiment that I would like to assign cell labels to. To accomplish this task, I used the Monaco reference database as input into SingleR based on the RNA expression data. I would now…

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Merge or integrate multiple samples and then do downstream analysis

I am doing some analysis on a public scRNAseq datasets in order to see differential gene expression between two clusters. The basal sample information about it: tissue_donor_1_treatment, tissue_donor_2_treatment, tissue_donor_1_control, tissue_donor_1_control, All of them produced under the same sequencing conditions. # In my opinion, I want to divide them into two…

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Bioconductor – ClusterFoldSimilarity (development version)

DOI: 10.18129/B9.bioc.ClusterFoldSimilarity   This is the development version of ClusterFoldSimilarity; to use it, please install the devel version of Bioconductor. Calculate similarity of clusters from different single cell samples using foldchanges Bioconductor version: Development (3.19) This package calculates a similarity coefficient using the fold changes of shared features (e.g. genes)…

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running for loop for resolution of seurat got error: Error: Not an S4 object.

Dear All fellows, I’m using SCTtransform to normalize data and try to run various resolutions to determine which one is good for clustering. However, once it comes to for loop sections, it shows me the clustering plot of resolution 0, but the rest was terminated with error saying that Error:…

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Postdoctoral Research Scientist job with ADARC

Description Dr. Zizhang Sheng’s lab at Columbia University Irving Medical Center, Department of Medicine, Division of Infectious Diseases, the Aaron Diamond AIDS Research Center (ADARC), applies bioinformatics and biochemical approaches to elucidate the mechanisms of humoral immune response to infection (HIV, SARS-CoV-2, influenza, malaria, etc.) and to understand the role…

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Visualize individual cell clusters colored by meta.data variable

Seurat: Visualize individual cell clusters colored by meta.data variable 0 Hello, I am analyzing a public scRNA dataset using Seurat. My goal is to observe variation inside individual cell clusters according to a condition (e.g. the diet) in a visual way using a dimensional reduction plot, e.g. observing sub-clusters of…

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Bioconductor – CDI

DOI: 10.18129/B9.bioc.CDI   Clustering Deviation Index (CDI) Bioconductor version: Release (3.18) Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be…

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Error when reading in loom files with loompy

I’m trying to import a loom file that I created using Seurat and loomR from 10X data, and I keep getting the same error. Here is my code: > import scanpy as sc > import loompy > print(loompy.__version__) ## 3.0.6 > adata = sc.read_loom(‘myloomfile.loom’) Here is the error message I…

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Create Seurat Object from matrix and two text files

In their methods they state it’s a matrix market format. And the count matrix is in MatrixMarket format. However, the file on GEO is missing the MM header. Usually the first (non %%) line will have the row number, column number, and number of non-zero values. This lets whatever reader…

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Reproducible seurat clustering

Dear all fellows, What is the standard way for reproducible Seurat clustering in single cell? I have been trying to use set.seed function like library(tidyverse) library(Seurat) library(patchwork) set.seed(198752) However, once it comes to running the following script, I get new shape of cluster all the time I rerun it. How…

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Testing the interaction term in single-cell RNAseq DEG analysis

Testing the interaction term in single-cell RNAseq DEG analysis 0 I wonder if there is a way to test for the “interaction term” in Seurat. I have two categorical variables and would like to know if the interaction between these two variables is significantly different in a scRNAseq (2 x…

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Postdoctoral Research Fellow, Computational Biology / Bioinformatics job with Visterra, Inc.

Summary Visterra is seeking a highly talented, self-motivated and innovative Postdoctoral Research Fellow to join our Technology Platform team. The fellow will lead the conceptualization and implementation of advanced machine learning approaches to large single cell, spatial and multi-omic datasets. The role will involve developing creative approaches to leverage machine…

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Help with cellchat error

Help with cellchat error 0 Hi Biostars, I try to use cellchat but got this error. Would you please have a suggestion? I just merge control and mutation sample to get a seurat object and haven’t do cell type annotation yet. Thank you so much! cellchat <- computeCommunProb(cellchat, raw.use =…

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Normalized data values very different from unnormalized counts in Seurat

Normalized data values very different from unnormalized counts in Seurat 0 I the sceasy R package to convert Burclaff et al.’s (2022) single-cell data (GSE185224) from scanpy H5AD data to a Seurat R object. My object’s UMAP looks similar to the authors, and I subsetted out “colon” samples. I then…

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Harmony with PHATE

Harmony with PHATE 0 Hi Bio-community, I integrated my single cell dataset using Harmony. Now Harmony only provides a new slot for the cell.embeddings in the seurat object, like pca. How can I utilize this embedding in a PHATE plot? How can I combine Harmony with PHATE? Best, Tolga Phate…

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Integration Seurat different healthy samples (fresh vs frozen)

Integration Seurat different healthy samples (fresh vs frozen) 0 Hi Bio-community, I am investigating a single cell dataset using the seurat workflow. In total I have 8 different samples, each from a different patient. 7 of them were frozen samples and S8 in the umap plot is the only fresh…

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Why I get different results from FindMarkers () while running the same script?

Why I get different results from FindMarkers () while running the same script? 0 Hi everyone, I am student that is approaching the omics field and I am running my first single-cell analysis in Seurat using a container. Recently, after a reboot of the server where my data is stored,…

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Doheatmap in seurat

Doheatmap in seurat 2 Hi guys (sorry I cannot show the full heatmap as it is about to be in a paper), I am trying to reorder this heatmap’s identity where instead of BGH>CFAP>NM>WT we have WT>CFAP>NM>BGH. How do I do that in doheatmap? Here is the code that gave…

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How to ‘organize’ multiple umap/genes generates with Seurat `FeaturePlot`in a specific way

How to ‘organize’ multiple umap/genes generates with Seurat `FeaturePlot`in a specific way 1 Hi, Do you know how to ‘organize’ multiple umap generates with Seurat FeaturePlotin a specific way? For example organize 4 plots all all vertically or horizontally instead of having them organised as 2×2 or only plot_grid is…

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Elucidata hiring Senior Bioinformatics Scientist in Bangalore, IN

About Elucidata Delivering ML-ready biomedical molecular data. Job Description Elucidata’s mission is to power drug discovery by harnessing the power of structured and unstructured biomedical data. Our state-of-the-art technology transforms data so that it is analysis-ready. Biomedical data is vast but unstandardized, hence it remains underutilized. Or as we say…

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Input data matrix from Seurat toolkit analysis for RNA velocity analysis using scvelo

Input data matrix from Seurat toolkit analysis for RNA velocity analysis using scvelo 0 Hi, I have done the scRNAseq analysis follwoing seurat toolkit vignette (SCTtransform + integrate + clustering) and now planning to run RNA velocity analysis using scvelo tool. Is it reasonable to use the SCT assay, data…

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unbiased clustering of these top 50 genes in seurat

unbiased clustering of these top 50 genes in seurat 0 Here is a code, i have now: combined <- rbind(mutant1, mutant2, mutant3) as.data.frame(combined) data_genes <- data.frame(gene = rownames(combined), combined, row.names = NULL) View(data_genes) data_genes %>% group_by(mutant) %>% mutate(abs_lfc = abs(avg_log2FC)) %>% top_n(n = 50, wt = abs_lfc) -> top50 I…

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How to remove the default title to a DimPlot() splitted into two by group.by ?

How to remove the default title to a DimPlot() splitted into two by group.by ? 1 Hi, Is it is possible to remove the default title (in the pic below “stim”) to a DimPlot() which is splitted into two by group.by.? I want to generate the same type of plot/pannel…

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fragments file generation via Sinto from CellRanger output

fragments file generation via Sinto from CellRanger output 0 Hi, I am following the instructions for the PASTA package (satijalab.org/seurat/articles/pasta_vignette.html). This package uses scRNA-seq data to infer alternative polyadenylation usage from scRNAseq data. It requires among many input files also a fragment file. The authors state the following must be…

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Integrating 10x scRNAseq and multiomics

Integrating 10x scRNAseq and multiomics 0 I am starting to work with some single cell sequencing data and I am trying to get my head around what the best pipeline is. I have 6 samples in total, 3 from control and 3 from a treated group. Of each, 2 were…

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A spatial sequencing atlas of age-induced changes in the lung during influenza infection

Single-cell RNA sequencing reveals cellular heterogeneity among young and aged lungs post-influenza infection In order to investigate age-induced alterations in the host response to influenza A virus (IAV) infection, we infected groups of three young (16–18-week-old) and three aged (80–82-week-old) female C57Bl/6 mice intranasally with 50 PFU of the PR8…

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seurat-creating heatmaps

seurat-creating heatmaps 1 I have three tables (results from differential expression in seurat): Table 1 is for mutant 1 vs WT Table 2 is for mutant 2 vs WT Table 3 is for mutant 3 vs WT I would like to create a heatmap that shows all the genes combined(mutant…

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Cannot add new cells with NormalizeData from seurat

Cannot add new cells with NormalizeData from seurat 0 Hi, I’m tried running NormalizeData with a seurat object created from raw matrix files of cellranger outs, however it returns an error: WT1 <- NormalizeData(object = WT1) Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [—-|—-|—-|—-|—-|—-|—-|—-|—-|—-|…

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Monocle3 transition to seurat

Monocle3 transition to seurat 1 I know to transition from Seurat to monocle3 one has to use library(Seurat Wrappers) and then use the function: as.cell_data_set(seuratobject). But, after reclustering in monocle3, i would like to go back to Seurat to perform differential analysis. How do i do this? How do i…

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QC cut off for snRNAseq data

QC cut off for snRNAseq data 1 Hi all, Apologies if this is a silly question as I am very early on in my bioinformatics journey! I have been playing with an snRNAseq dataset in Seurat and I am currently performing QC on the dataset. Alot of the profiles look…

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Bioconductor – nipalsMCIA (development version)

DOI: 10.18129/B9.bioc.nipalsMCIA   This is the development version of nipalsMCIA; to use it, please install the devel version of Bioconductor. Multiple Co-Inertia Analysis via the NIPALS Method Bioconductor version: Development (3.18) Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the…

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r – Complication with clustree image generation

Running the below code (initially without par (lwd = 1) line ) returned the following error, and the same error was returned again after setting par(lwd = 1) or to 0.5 or 10. Truthfully don’t totally understand what’s going on when i change that variable other than that id be…

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Code for reading h5ad files in R

Code for reading h5ad files in R 1 How can I read and view h5ad files in R? I tried the Seurat package but I see no function that can read such files. I found another package called SeuratDisk but it’s confusing. Say I have a file called GSE123456.h5ad, how…

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Differential gene score in single cell experiment

Hello Biostars’ community, long time not posting here, hope you are all doing well 🙂 I have a single cell multiome (RNA+ATAC in the same nuclei) experiment, made of 20 samples across 4 time points (tpCtrl,tpA,tpB,tpC) of a disease. At a more advanced stage of my analysis, I am not…

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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…

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How to create a panel figure where group of violin plots generated with Seurat are distributed with a specific distribution

Hi, I know it’s stupid question but I cannot figure it out. I have a scRNAseq dataset integrated (treatment vs control) and I need to show specific genes as violin plots showing the difference between the two condition only for a subset of cell types/cluster. However I have make one…

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GEO Dataset: Difficulty Understanding Matrices, Compliation

GEO Dataset: Difficulty Understanding Matrices, Compliation 1 Hi, I am new to using GEO, novice at R (have used seurat for my own scRNA data), apologies for how basic this question is: I am trying to replicate figure 1 from a recent paper using seurat. They’ve deposited their data as…

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Seurat changing order cluster shown in the violin plot

Hi, I have scRNAseq with total of 33 clusters and I want to select only few of them (eg. cluster 0,3,6,7) and plot specific genes in a violin plot. However ideally I would like to have the clusters shown in specific order in the violin plot (eg. cluster 7,3,6,0) and…

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Ribosomal cluster

Ribosomal cluster 0 Hi Biostars, I work on single cell data and got this issue hope you can help. I got a cluster has many ribosomal genes. So what can we say about this? I think error with sample preparation. Thank you so much! I found a relevant post here,…

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2 dimensional quadrant plot

2 dimensional quadrant plot 0 Hey everyone, I am working with single cell RNA seq data and I am trying to create one of the plots but I am unable to. I am fairly new to this, I am using R studio to make this plot. nihms-1532254-f0004.jpeg I have a…

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Is Guix full-source bootstrap a lie?

One of the biggest concern, in my humble opinion, about the current state of this awesome story is non-deterministic compilations. And especially at early stages, for example gash-boot. $ guix build -e ‘(@@ (gnu packages commencement) gash-boot)’ $ guix build -e ‘(@@ (gnu packages commencement) gash-boot)’ –check guix build: error:…

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Can’t find a gene in single cell

Can’t find a gene in single cell 0 Hi Biostars, I have single-cell data with wild type and knock-out gene A. When I open the loupe file of both wild type and knock-out, I can find gene A in both samples. However, when I use Findallmarker() on the Seurat object…

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Create seurat inputs without cellranger

Create seurat inputs without cellranger 1 “Hey there! I’m really curious about creating Seurat inputs without using Cell Ranger, as we’ve got our own sequencer and have done the sequencing in-house. Has anyone else tried this approach or can offer some guidance on how to go about it? Any help…

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How to read tsv data as dgcmatrix

How to read tsv data as dgcmatrix 0 Update: Solved. The barcodes provided in the metadata and count matrix are not the same. One is “xyz-1”, another is “xyz.1”. Just need to correct the barcodes. I will post some photos later as references for people who might encounter similar issues…

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Cacoa with Seurat analysis

Cacoa with Seurat analysis 0 Hi everyone, Has anybody tried to run Cacoa with Seurat object? Can someone explain sample.per.cell argument, what it contains? what does one extract the embedding from Seurat object ? I get an error saying dimensions should be positive with Cacao. I have also posted the…

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DotPlot error in Seurat

Dear All, Sorry for another question. I have seurat integrated object, which was annotated with cell types and have three conditions with 3 sample per condition. I would like to replicate some codes in seurat, but was error Error: None of the provided identity class levels were found and not…

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Picking optimal resolution for single cell in seurat pipeline

Picking optimal resolution for single cell in seurat pipeline 1 Dear all fellow members, as I progressed into single cell analysis, one question that I would like to ask is how do we know the optimal resolution we should pick for our data as cluster will change once the resolution…

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When should I NOT apply batch correction for my single-cell RNAseq data?

Hi! Some personal thoughts/opinions: integration is about finding the similar cell types/states across data sets (either with or without batch effect). An experimental batch corresponds to a set of samples that were processed simultaneously in the same manner and, thus, reducing the effect of technical artifacts/noise. As I see your…

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Feature plot not applicable for RunTSNE object in seurat?

Feature plot not applicable for RunTSNE object in seurat? 1 Dear All, I visualized my cluster using tsne object (image attached) and would like to run FeaturePlot to examine the expression of particular gene, but it did not work for tsne object. I could only do it with UMAP. Any…

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Filter, Plot, and Explore with Seurat in RStudio

First thing’s first, we need to load the packages we will be using. In order to use any functions of a package, we must first call the library of that package. In your console (likely in the lower left corner of your RStudio window), run the following lines of code…

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Transfer harmony-integrated scRNA-seq data to scanpy

Transfer harmony-integrated scRNA-seq data to scanpy 1 I have integrated two scRNA-seq datasets using harmony method. Unlike Seurat integration, Harmony just adds extra embeddings for further clustering and other analysis. However, the data (raw counts, normalized, and scaled slots) is the same as in unintegrated data. So, when I transfer…

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Bioinformatics Jobs for September 2023

Bioinformatics is an ever-evolving field of science that uses computing and statistical techniques to analyze and interpret biological data, such as DNA and protein sequences, gene expression levels, and metabolic pathways. With the help of a Bioinformatics Developer, you can solve complex problems associated with biomedicine, biotechnology, drug discovery and…

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Subclustering of intergated cells from scRNA-seq data

Subclustering of intergated cells from scRNA-seq data 1 I used SCTnormalization and Seurat integration to integrate 3 scRNA-seq datasets. After manual annotation using RNA assay, I have one particular cluster of cells with overexpressed different T cells markers. So, to find heterogeneity of T cells I subclustered that particular cluster:…

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Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas | Acta Neuropathologica Communications

Single-nuclei RNA-sequencing analysis of NF1-associated plexiform neurofibroma reveals specific non-neoplastic and neoplastic cellular subpopulations Single-nuclei RNA-sequencing (snRNA-seq) was performed on 8 bulk frozen PN patient samples capturing approximately 4,000 nuclei per sample, a sufficient number of nuclei to provide adequate coverage to report the high levels of cellular heterogeneity found…

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Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas

doi: 10.1186/s40478-023-01639-1. Vladimir Amani  1   2 , Kent A Riemondy  3 , Rui Fu  4 , Andrea M Griesinger  5   6 , Enrique Grimaldo  5   6 , Graziella Ribeiro De Sousa  5   6 , Ahmed Gilani  7 , Molly Hemenway  6 , Nicholas K Foreman  5   6 , Andrew M Donson #  5   6…

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Clustering in single cell

Clustering in single cell 0 Hi Biostars, When I read articles or tutorial about clustering in single cell, I noted that the clusters clearly separate. However, in my analysis, clusters of each cell types are not clearly separate even though I tried different clustering algorithms (louvain, leiden) or sctransform for…

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comparision of umap single cell

comparision of umap single cell 0 Dear Fellow, I’m currently learning to analyze single cell RNAseq and compare my result with the analysis by bioinformatician. We analyzed the same data of 9 individual patients from 10X. His UMAP looks nice, but mine looks a bit messy and aggregated together. I…

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How to determine the total count for each gene in lymphotype B

How to determine the total count for each gene in lymphotype B 0 Hello I really need help!! I don’t speak English very well so sorry I have RDS object, this file is processed, normalized (using sct transform approach) and clusters were identified (in other words it ready to use…

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Is it normal if regress out the cell cycle effects but the DEGs are quite the similar (no big changes)

Is it normal if regress out the cell cycle effects but the DEGs are quite the similar (no big changes) 0 Dear experts, Is it normal after regressing out the cell cycle effects but the DEGs are quite similar (no big changes)? The scRNAseq data are from one cell type,…

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Integrated Seurat object change name of the two conditions

Integrated Seurat object change name of the two conditions 0 Hi, I have a scRNAseq integrated seurat object composed by my control and my treatment. On this object I did all the analysis and I have all the plots needed (umap etc). Now it has been asked to use different…

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