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Fail to download resources

2

Hi all, I fail to download TF files resources and find I can't open https://resources.aertslab.org/. I'd like to know if there are other ways to download these important feather files?...

Hi All, I have two bone marrow samples, one from normal person the other form cancer patient. And I want to see there Monocytes. I've already know that BM from...

Fail to install velocyto

1

Hi, I'm new to python and I met a problem during installation. Can anyone give me some advice? Maybe I should try to install pysam first? ``` /xtdisk/miniconda/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: skipping incompatible...

error when using assay()

1

Hi, I got error every time when I try to get count assay from TENxPBMCData, and it doesn't happen before. Here's my code: ``` # BiocManager::install('TENxPBMCData') # (286 KB) library(TENxPBMCData)...

Hi, I'm new to kallistobustools and I want to use this powerful tool to pre-processing 10xscRNA-seq data for RNA Velocity. I've read the Tutorials of this tool but still confused...

Hi, all As new to scanpy, I met strange things when using `sc.read_csv`, the `obs` are genes and the `var` are cells ``` adata = sc.read_csv(x) data # AnnData object...

Hi dynamo group, I'm learning dynamo following the tutorial and I'm confused of the result of this code: ``` dyn.pl.jacobian(adata, regulators=['tfec'], effectors=['pnp4a'], basis='umap') # https://dynamo-release.readthedocs.io/en/latest/notebooks/Differential_geometry.html ``` I don't know how...

Unable to download sample data

2

Hi, dynamo group I'm learning dynamo following the tutorial, but sometimes it's hard to download sample data especially when I stay at home. ``` >>> adata = dyn.sample_data.zebrafish() |-----> Downloading...

Hi, I got strange error when running RunQuantileNorm of seurat-wrappers. ``` data.combined % RunQuantileNorm(split.by = "orig.ident") # Error in ncol(object@H[[1]]) ``` Just the same as this question: https://github.com/welch-lab/liger/issues/187 Any advise...

Error when running SpatialDimPlot

7

Hi all, I got an error when running https://satijalab.org/seurat/articles/spatial_vignette. Here's the code: ``` p1