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Commits on Jul 17, 2024

• Merge pull request #6 from EngreitzLab/VM_dev

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  kanghelen

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  58d066a

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Commits on Jun 21, 2024

• updating periodic changes

  

  Helen Kang

  committed
  4ca5c7d

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Commits on May 28, 2024

• tremendous speed up for the prepare step

  

  Helen Kang

  committed
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Commits on May 8, 2024

• Adding recent edits

  

  Helen Kang

  committed
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Commits on May 1, 2024

• committing recent changes

  

  Helen Kang

  committed
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Commits on Apr 18, 2024

• adding updates to automatically source ~/.bashrc in shell scripts, and adding updates to parallelize running multiple samples for seuruat_to_h5ad and batch_correlation rules

  kanghelen

  committed
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Commits on Apr 14, 2024

• adding updated conda/mamba environment configuration .yml file

  

  Helen Kang

  committed
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Commits on Apr 13, 2024

• updating cnmf_env's anndata package

  

  Helen Kang

  committed
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Commits on Mar 6, 2024

• fixing permanent paths

  

  helen

  committed
  0bd7d0c

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Commits on Sep 4, 2023

• adding recent updates

  

  Helen Yihua Kang

  committed
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Commits on Aug 18, 2023

• adding recent changes and updating sample config file

  

  Helen Yihua Kang

  committed
  ec30c67

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Commits on Aug 6, 2023

• adding recent updates: manual parameter in config for cell quality filter, fixed edge cases for Seurat inputs, and fixed comprehensive program output xlsx file for annotation

  

  Helen Yihua Kang

  committed
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Commits on Jul 7, 2023

• adding latest updates

  

  Helen Yihua Kang

  committed
  575c66b

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Commits on Jul 3, 2023

• added organism flag to rules and scripts

  

  Helen Yihua Kang

  committed
  39ac3e2

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• in the progress of adding organism flag

  

  helen

  committed
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Commits on Jun 30, 2023

• Editing README

  

  helen

  committed
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• Adding more V2G2P overview figures and explanations

  

  helen

  committed
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• Adding V2G2P overview figures to README file

  

  helen

  committed
  3e6fbd9

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Commits on Jun 17, 2023

• fixing logical error at TopicSummary rule

  

  Helen Yihua Kang

  committed
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Commits on Jun 16, 2023

• resolving edge cases

  

  Helen Yihua Kang

  committed
  de9a88a

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Commits on Jun 15, 2023

• committing recent small changes

  

  Helen Yihua Kang

  committed
  2ceb7ad

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Commits on Jun 13, 2023

• updating rules and Snakefile to avoid pipeline confusing 10X input with .h5ad input when only one is available

  

  Helen Yihua Kang

  committed
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• updating a more concise fix to prevent snakemake inferring input .h5ad file name recursively

  

  Helen Yihua Kang

  committed
  3d4cc27

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• adding helper cNMF_pipeline rules to avoid inferring file names recursively

  

  Helen Yihua Kang

  committed
  f37c36b

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• updating cNMF_pipeline rules to avoid inferring file names recursively (.raw.h5ad)

  

  Helen Yihua Kang

  committed
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Commits on Jun 12, 2023

• adding temporary fix for enhancer and promoter motif enrichment input file format

  

  Helen Yihua Kang

  committed
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• fixed error caused by sparse matrix in computing variance explained

  

  Helen Yihua Kang

  committed
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Commits on Jun 11, 2023

• updating to latest version

  

  Helen Yihua Kang

  committed
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• force merge with the latest version in branch fix_PoPS

  

  Helen Yihua Kang

  committed
  15af8d2

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• updating to latest code

  

  Helen Yihua Kang

  committed
  eb1c9ea

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Commits on Jun 9, 2023

• adding latest chagnes

  

  Helen Yihua Kang

  committed
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Commits on Jun 5, 2023

• debug commented out files not needed in Snakefile

  

  Helen Yihua Kang

  committed
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• test commented out Seurat object rules

  

  Helen Yihua Kang

  committed
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• updating README file

  

  Helen Yihua Kang

  committed
  4e4d8b4

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• updating README file

  

  Helen Yihua Kang

  committed
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