convert seurat to scanpy
Contents
convert seurat to scanpy
singlecell seurat(RDS) to scanpy(h5ad)
R code
library(Seurat)
library(SeuratDisk)
srt <- readRDS('subDC.rds')
# convert factor to character
i <- sapply(srt@meta.data, is.factor)
srt@meta.data[i] <- lapply(srt@meta.data[i], as.character)
DefaultAssay(srt) <- 'RNA' # set default assay
SaveH5Seurat(srt, filename = 'srt.h5seurat', overwrite = TRUE)
# if SaveH5Seurat get err:
# Object too old to save, please update your Seurat object to at least v3.1.2 using UpdateSeuratObject
# srt <- UpdateSeuratObject(srt)
Convert('srt.h5seurat','srt.h5ad', assay='RNA', overwrite = TRUE)
download test data
curl -o local.rds "https://corpora-data-prod.s3.amazonaws.com/6deef5dc-d572-4990-971d-b0380850ea55/local.rds?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=ASIATLYQ5N5XTBTXPXTJ%2F20221213%2Fus-west-2%2Fs3%2Faws4_request&X-Amz-Date=20221213T024129Z&X-Amz-Expires=604800&X-Amz-SignedHeaders=host&X-Amz-Security-Token=IQoJb3JpZ2luX2VjEIb%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLXdlc3QtMiJIMEYCIQCbLFp40OW8T47mtmQF560aKt8j3nv1KTI2lB%2FmbuUMuQIhAMIcHizLCt0M%2BYr7Rb63hLM4Dx4jbcNaeP2m90KJDbW1KvQDCK%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEQARoMMjMxNDI2ODQ2NTc1IgxqTq9d1N0QQSHNnu0qyAMzuvesva8WIsuIpaTgLk%2BUhus3cnrycc0Q%2F%2BKF9DUYmW7MIIBu20dkqvVw9ZAeqXHoiVn7YHG21gytN4AZFqPv7aeuD%2FPM6mgUgBzUDRQHvFznNdd8%2FNTqwT0obN9ULKbyhj%2BtR1U8SG4gaAJpqayit8LfYNkg9rAk8xYEN6V%2BfSl8DywC%2BNCkaMfGa0MO3uVXv6Zw%2FZCvfKoLkQol8TOhIaB77P2w4%2F68THY7ET9Um9vIkTR44fSw%2Fs0eNt2nFe9PxcM%2B2JfrsQg%2BdRKXCztwq08Ak5YhRYDDAlcGkC%2Bg1elay0VbFftBrDQJaW9rPvIkyWp1TFzCXBP3x3ZnU0gSew2h7A05%2BTsDtAMkYDiEHGubT65fIOQ6e0z4FFFK2UmaZfqjXd3VIreh2pNY98LFQ0LiFEFWbUA8mpXzEYrvHiElFmQoPXOQ8RNCYn%2BQZAaPd6TmbqPHsrQhL9MN7JHm%2BcQkjJAB%2BIeAf4PSTHEcyr4Ja70a5BaEPJIAICxjIgAEQW%2BYk5oUuzRpjVzNFDtiKD99Ia%2F5hna%2B%2BOwEKiO6D%2F9n0e%2F1IMQ2XnFBv%2FM%2B5cHSMKEQ8wpV3FizwvI7yVRSjGgEBG3F5ykwxcvenAY6pAHJRSf5Q7vwtVMCCaKoDxD4C5XJzj6NV2V2XPnugcvg5vNaBcN2N9mxD%2B5X19FwM%2BkQ9%2FOVylXh20zIKtiDlMy9RGFoO2jNnf5mfQMXKD8Q7i8nK8F11Bw949QL69dY2fQJX5T%2Be8EeA8JPPIn3k14Hhru3iQTQmb9OVyOU8R3c9BC4qkwldkVSW8k3iMsu0OM%2BCEGxw0pCxkKBZZp1FW9BI8MFYA%3D%3D&X-Amz-Signature=66a9478d223bd6f0947a23594df48447f2628d2130ec9f0316d6c14f7ac3ce99"
[6]:
library(Seurat)
library(SeuratDisk)
srt <- readRDS('/Users/yuanzan/Downloads/local.1.rds')
i <- sapply(srt@meta.data, is.factor)
srt@meta.data[i] <- lapply(srt@meta.data[i], as.character)
DefaultAssay(srt) <- 'RNA'
srt <- UpdateSeuratObject(srt)
SaveH5Seurat(srt, filename = 'kidney_tumors.h5seurat', overwrite = TRUE)
Convert('kidney_tumors.h5seurat','kidney_tumors.h5ad', assay='RNA', overwrite = TRUE)
Validating object structure
Updating object slots
Ensuring keys are in the proper strucutre
Ensuring feature names don't have underscores or pipes
Object representation is consistent with the most current Seurat version
Creating h5Seurat file for version 3.1.5.9900
Adding counts for RNA
Adding data for RNA
No variable features found for RNA
Adding feature-level metadata for RNA
Adding cell embeddings for pca
No loadings for pca
No projected loadings for pca
No standard deviations for pca
No JackStraw data for pca
Adding cell embeddings for umap
No loadings for umap
No projected loadings for umap
No standard deviations for umap
No JackStraw data for umap
Validating h5Seurat file
Adding data from RNA as X
Transfering meta.features to var
Adding counts from RNA as raw
Transfering meta.features to raw/var
Transfering meta.data to obs
Adding dimensional reduction information for pca
Adding dimensional reduction information for umap