Thursday, February 27, 2025

pip install does not seem to install software

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First find which python is being used  import sys print(sys.executable) # /usr/bin/python3 -m pip install palantir --force-reinstall
Friday, November 22, 2024

R package installation error: API rate limit exceeded for

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  Error: Failed to install 'unknown package' from GitHub:   HTTP error 403.   API rate limit exceeded for XXXXX. (But here's the...
Monday, October 21, 2024

SCENIC - GRN prediction time

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Memory : 256 gb RAM !pyscenic grn {loom_path} {tfs_path} -o $outpath_adj --num_workers 56 Sending large graph of size : 144.10 MiB took less...
Tuesday, May 14, 2024

Troubleshooting Module Import Issues in Jupyter Notebook

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--------------------------------------------------------------------------- ModuleNotFoundError Traceback (most rece...
Tuesday, February 20, 2024

How to Access SMB Shares on Linux: A Step-by-Step Guide

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If you're working in a mixed environment where you need to access shared folders (also known as SMB shares) from a Windows machine on yo...
Thursday, February 15, 2024

Resolved - TypeError: Can't implicitly convert non-string objects to strings

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When trying to save my adata object: adata_query_final.write_h5ad("anndata_objects/3_pcls_adata_with_scArches_labels_20240215.h5ad...
Monday, January 15, 2024

Resolved - R Shiny - Navigation containers expect a collection of

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An error has occurred! Navigation containers expect a collection of `bslib::nav_panel()`/`shiny::tabPanel()`s and/or `bslib::nav_menu()`/`sh...
Friday, January 12, 2024

Resolved - Souporcell installation issues

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 $ bash run_Donor_Deconvolution.sh checking modules imports done checking bam for expected tags [W::hts_idx_load2] The index file is older t...
Thursday, January 4, 2024

Resolved - Issues with running Monocle 3

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I converted my adata to rds format using sceasy first since I cannot use the anndata object directly in R, specifically monocle 3. Issue 1: ...
Wednesday, January 3, 2024

QA on in Single cell data analysis

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Question 1: I have adata object which does not have layers with spliced and unspliced counts information. Is it even possible one of the ker...