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Version 2 Update#5

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chenv3 merged 26 commits intomainOpenOmics/cell-seek:mainfrom devOpenOmics/cell-seek:devCopy head branch name to clipboardApr 19, 2024

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Commits

Commits on Dec 18, 2023

• Edit GEX seurat QC report to keep cluster resolutions in correct order

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• Initial addition of seurat summary QC report for GEX

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Commits on Mar 20, 2024

• seuratSampleQC.R - Fix bug that made cut-off line not plot

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Commits on Mar 22, 2024

• Initial commit with edits to add rename flag for GEX pipeline

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Commits on Mar 29, 2024

• Adding in support for different versions of cellranger (GEX, CITE, VDJ, MULTI) and the 10x newly released 2024 references. Changing version flag to pipeline to avoid confusion, and adding in cellra…

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• Add newly required flag to multiConfig rulee. Edit typo in write_multiconfig.py

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Commits on Apr 1, 2024

• write_multiconfig.py - edited to always have 3 columns for CMO info

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Commits on Apr 2, 2024

• Merge pull request #3 from OpenOmics/main

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Commits on Apr 3, 2024

• Merge branch 'dev' of github.com:OpenOmics/cell-seek into dev

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• seuratSampleQC.R - add metadata parameter to be able to add sample level metadata when performing initial QC and output sessionInfo log file

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• generateSummaryFiles_MULTI.py - Edited to add a Fastq sheet to report FASTQ related statistics reported in multi metric summary

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• seuratSampleQCSummaryReport.Rmd - edit method of creating report tables, add UMAP filter plot

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• gex.smk - Fix sample list in rule seuratQCSummaryReport

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Commits on Apr 5, 2024

• gex.smk - Edit to add in metadata file, and fix formatting for sample list in seuratQCSummaryReport

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• Edit cell-seek, run.py, Snakefile

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Commits on Apr 9, 2024

• seuratSampleQCSummaryReport.Rmd - fix to keep samples ordered in report

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• cell-seek - Add genome option

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• Update documentation and bump version

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Commits on Apr 16, 2024

• Add QC percent.mito vs nFeature plot and silhouette plot, edit filtered UMAP

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Commits on Apr 17, 2024

• Copy QC reports to final reports folder, edits to reports and documentation

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• seuratSampleQCSummaryReport.Rmd - Change header names

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• Update test to match new required flags

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• Update README.md

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• Remove local rule

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• Remove local rule

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Commits on Apr 18, 2024

• Add rename flag to VDJ and ATAC pipelines, fix VDJ mm2024 genome entry

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