STREAM

STREAM copied to clipboard

Stream 1.1 Error

6

Hello, I'm having trouble upgrading the version of STREAM. While before I had no errors, now none of my scripts work. I work with conda environments and here is the...

bellenger-l

First thanks for the nice tool! I was trying to mapping two scATAC-seq data, eg, ko to wt, with stream v1.0 In both datasets I used the precomputated UMAP projections....

ccshao

import stream as st st.__version__

4

Dear， Thank you for this good package, well, I can install this successfully, but when I run the jupyter I cannot even import stream as st. Always returns to "The...

sailseem

my code is : import stream as st adata=st.read(file_name='/outs/filtered_peak_bc_matrix/matrix.mtx', file_sample='/outs/filtered_peak_bc_matrix/barcodes.tsv', file_feature='/outs/filtered_peak_bc_matrix/peaks.bed', file_format='mtx',workdir='./result_atac') adata.var.index =adata.var[0].astype(str) + '_' + adata.var[1].astype(str) +'_' + adata.var[2].astype(str) st.cal_qc(adata2,assay='atac') the error is : ValueError Traceback (most recent...

tianchen2019

Issue with installation

12

Hi there, I'm using Miniconda3 with Python 3.8.3 on win32, I'm relatively new to Python though as I've always worked in R. When I try to install STREAM as suggested:...

hemadelon

Issue with selecting cell types in the STREAM

2

Hello, I have already annotated object from SCANPY that I am trying to use in the stream. But I can't select and visualize cell types from my data while making...

Pawan291

h5Seurat format

8

Hi, is it possible to use h5Seurat format converted by SeuratDisk in STREAM? https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html My data is integrated seurat object.

wajm

a legend bug

3

recently i find a bug in core.py the raw code is : ax_i.legend(handles=legend_handles[1:], labels=legend_labels[1:], code in this way will loss the first legend label i change the code into ax_i.legend(handles=legend_handles[0:],...

wangli-sh

st.add_cell_labels error: ValueError: Length mismatch

10

Hi, I'm using a loom file saving from a seurat object. My adata is like: AnnData object with n_obs × n_vars = 56109 × 22965 obs: 'ClusterID', 'ClusterName', 'DF_classification', 'RNA_snn_res_1_5',...

XYZuo

`uns_key` has no default`

1

To recreate using https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3674239, ``` import stream from scipy.io import mmread import pandas as pd name = 'GSM3674239_b1' x = mmread('data/' + name + '.matrix.mtx') gene_names = pd.read_csv('data/' + name...

BioTechTimy