Tag: H5AD

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

Mouse breeding and husbandry All experimental procedures related to the use of mice were approved by the Institutional Animal Care and Use Committee of the AIBS, in accordance with NIH guidelines. Mice were housed in a room with temperature (21–22 °C) and humidity (40–51%) control within the vivarium of the AIBS…

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cellphonedb results visualization

I want to visualize cellphonedb results but I get several error. I do visualization by ktplotspy package. First, I read the required files based on its tutorials and when I try to create the heatmap, it gives an error: code: kpy.plot_cpdb_heatmap( adata=adata, pvals=pvals, celltype_key=”celltype”, figsize = (5,5), title = “Sum…

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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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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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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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How to import filtered_tf_bc_matrix and add it to my anndata object?

Hello, I am analyzing some ATAC samples and I would like to add the motif information to my objects. So far I have imported my fragment files and clustered the cells. I would like to add the filtered_tf_bc_matrix information so I can do differential expression based on the motifs but…

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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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scanpy problem for empty cells

Hello everyone, I encountered a problem when I use scanpy analysis my data. When I tried to remove scrublet, and then I encountered following error: filtered out 42144305 cells that have less than 200 genes expressed Running Scrublet normalizing counts per cell /rsrch4/home/canbio/conda/envs/scvi-env/lib/python3.11/site-packages/scanpy/preprocessing/_normalization.py:197: UserWarning: Some cells have zero counts warn(UserWarning(‘Some…

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How to implement the code in MonkeyBread package

I get the following error when I want to implement this : (older_path=”/Users/Desktop/MonkeyBread adata = mb.util.load_merscope(folder_path) … reading from cache file cache/Users-pedram-Desktop-MonkeyBread-cell_by_gene.h5ad) KeyError Traceback (most recent call last) Input In [16], in <cell line: 2>() 1 folder_path = “/Users/pedram/Desktop/MonkeyBread’ —-> 2 adata = mb.util.load_merscope(folder_path) File ~/opt/anaconda3/lib/python3.9/site-packages/monkeybread/util/_load_merscope.py:74, in load_merscope(folder, use_cache, cell_bounds,…

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In Scanpy, how to RDS file and merge it with other Scanpy objects.

In Scanpy, how to RDS file and merge it with other Scanpy objects. 0 I have an RDS file that includes several Seurat objects that I want to use. I want to read it into scanpy and merge it with another file. What I did was convert the RDS file…

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h5ad cellxgene to R

I am trying to bring this small dataset (1496 cells, 43MB) from cellxgene. 1 R SeuratDisk h5ad to h5seurat and then to seurat. library(SeuratDisk) SeuratDisk::Convert(“local.h5ad”, dest = “local.h5seurat”, overwrite=TRUE) g <- SeuratDisk::LoadH5Seurat(“local.h5seurat”, meta.data=FALSE, misc=FALSE) Validating h5Seurat file Initializing RNA with data Adding counts for RNA Adding feature-level metadata for RNA…

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from seurat to scanpy data conversion and re-scaling

Hello everyone I am working on spatial transcriptome data . For analysis I used seurat R package. Specifically, I’ve been working with 4 samples that have a batch effect. To integrate them, I) I used the anchor-based integration method along with SCT normalization. II) From clustering analysis, I found some…

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Analysis a scRNAseq object that already has cell type annotation

Analysis a scRNAseq object that already has cell type annotation 0 Hi all I have recently downloaded a publicly available scRNAseq dataset that I want to analyse. The goal will be to do some differential expression analysis between two specific cell type clusters. The raw file was in .h5ad format,…

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RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

RevGel-seq sample preparation workflow Experiments were performed with the RevGel-seq protocol, capable of analyzing 10,000 input cells per sample with the specially designed gelation device (Fig. S3). The individual steps shown in Fig. 1A, from cell-barcoded bead coupling to library preparation for sequencing, are more fully described below: Cell labeling Cells…

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How to include spatial coordinate data into anndata within scanpy

Hello I am working on 10X visium spatial transcriptome data which was processed in seurat pacakge with image data. For my downstream analysis, I am trying to import seurat normalized data into scanpy. For this I converted seurat object to h5ad using these steps. SaveH5Seurat(test_object, overwrite = TRUE, filename =…

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Analysis of Smart-Seq3 data with kallisto-bustools

Tutorial:Analysis of Smart-Seq3 data with kallisto-bustools 0 Based on @dsull’s answer. The smart-seq3 analysis is handled by the kallisto-bustools pipeline. Create a conda environment if needed. Create the conda environment file and save it as env_kb.yml. # conda environment for kallisto bustools pipeline name: kb channels: – bioconda – conda-forge…

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scRNAseq analysis – h5ad file conversion to Seurat format

scRNAseq analysis – h5ad file conversion to Seurat format 0 Hi all. I have a single .h5ad file that contains scRNAseq data from several samples. I would like to convert it so that I can open it in Seurat (I am comfortable with R, but not with Python). I have…

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Single cell database scrna dB for bioinformatics database development (1)

Single cell database construction High quality integrated single cell database If readers just want to get a ready-made single-cell database with rich content and add it to their own PC or linux The server , You can skip the following detailed theoretical tutorial Database download link : Click to download…

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Obs_name

Obs_name 0 Can someone please help explain what the Obs_name represents? I exported the anndata matrix (h5ad) and attempted to transform it to the Seurat object using something similar to the following: exprs <- t(adata$X) colnames(exprs) <- adata$obs_names$to_list() rownames(exprs) <- adata$var_names$to_list() # Create the Seurat object seurat <- CreateSeuratObject(exprs) #…

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Best compression for single cell RNA-seq object

Best compression for single cell RNA-seq object 0 I generated a scRNA-seq object (counts, PCA, UMAP embeddings, DEGs etc.) in Scanpy or Seurat. What is the best data structure to store this in to reduce the size of the object? I’m considering H5AD (scanpy/anndata), RDS or H5Seurat (Seurat), or Loom…

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