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down sampling in st.map_new_data

2

Hi stream team, When performing the stream.map_new_data, I guess that the cells from two different stream objects are not down sampling to get equal number of cells? This might lead...

ccshao

When I run the code ,st.subwaymap_plot_gene(adata,root='S0',genes=['CD8A']) ,I got the error: ValueError: 'c' argument must be a color, a sequence of colors, or a sequence of numbers, not TGCACCTTCAGCTGGC-3 And I...

yejg2017

AttributeError: 'Graph' object has no attribute 'node'

2

yejg2017

Mapping KO data to trajectory built from WT data

6

Hi, I have scRNA-seq data from two conditions: WT and KO. I would like to build a trajectory based on WT data and then map KO data to the WT...

leiliuC

jaspar2016

1

Hello there, Thanks for providing this amazing tool for single-cell analysis..I am running the stream_atac function on command line but it says that it cannot install the R package JASPAR2016....

Brawni

Mapping feature using scATAC-seq data

5

Hello, I have been trying to use the mapping feature on two different scATAC-seq datasets. Both are able to infer trajectories individually. However, when trying to use the mapping feature...

carmenpetitjean

Are there plans to provide `scanpy` integration? Since both are based on `anndata` it should not be too difficult, but it would be nice to be able to load an...

chris-rands

AttributeError: 'SpectralEmbedding' object has no attribute 'transform'

6

Hi: Sorry for bother you again. When mapping the new data set to the reference, error happened. Command lines: 1. Generating reference stream.select_variable_genes(wt) stream.dimension_reduction(wt, n_jobs=4) stream.seed_elastic_principal_graph(wt) stream.elastic_principal_graph(wt,incr_n_nodes=10, epg_alpha=0.03, epg_trimmingradius=0.1) stream.optimize_branching(wt)...

jipeifeng

Issue with finding variable genes

6

Hello, I am using anaconda3 on a Windows10 machine with Spyder interface to run Stream. When I try to use my data to identify Variable genes, I get the following...

SathiyaNManivannan

Issue with mapping step

2

Hi: I have followed the pipeline to mapped another group of cell to the reference. Then, the result was so strange. (I have generated the reference using 'umap' to reduce...

jipeifeng