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Commits on Mar 29, 2021

• Tweak visualization of Clue hits

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• Factor out generation of gene sets and clue query in separate scripts

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• Use new deseq files

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• Fix metadata of LINCS 2020 CMap dataset

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• Redo read depth table

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Commits on Mar 19, 2021

• Update DESeq2 analysis with new metadata, use QS files

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• Wrangle new LINCS 2020 CMap data

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• Add missing time for experiments, use qs

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Commits on Feb 12, 2021

• Visualize connection of unknown compounds with genetic pertubations on CMap

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Commits on Jan 22, 2021

• Add controls to CMap results heatmap with unknown compounds

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Commits on Jan 15, 2021

• Add violin plots for sequencing depth

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• Add clue query for ribo and palbo alone

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• Add deseq analysis of bulk data

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• Split heatmap of unkown compounds versus genetic pertubations in two horizontally

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Commits on Oct 23, 2020

• Redo Clue query using more principled approach

  clemenshug

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• Add visualization of CMap hits for compounds not in Cmap

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Commits on Sep 9, 2020

• Increase wall time to 30min

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• Include replicates in DGE datasets. Rewrangle deseq input to take into account replicates

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Commits on Sep 8, 2020

• Pick represantitve genes for correlation plot. Shade background areas separately

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• Query clue using new DESeq2 results

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Commits on Sep 1, 2020

• Redo differential expression more systematically

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Commits on May 29, 2020

• Add all gene sets to synapse

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• Add CMap queries using single cell lines and only measured L1000 genes

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Commits on May 13, 2020

• Query with CMap signatures using multiple z-score cutoffs

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• Fix aggregating drug treatments across datasets for DESeq2

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Commits on May 12, 2020

• Re-wrangle CMap data to new SMS version including comparison of masses

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Commits on May 6, 2020

• Re-run DESeq2 with drugs aggregated across all different datasets

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Commits on May 1, 2020

• Prepare deseq input using new lspci_ids

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• Rewrangle DGE data using new lspci_ids and fix some lscpi_id drug name mappings by manually editing their names

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Commits on Apr 14, 2020

• Fix imports and data set names

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• Refactor clue connectivity analysis, split data prep and plotting

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Commits on Apr 1, 2020

• Add dose-response analysis for DGE vs L1000

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• Bulk

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Commits on Feb 27, 2020

• Fix DESeq2 of treatment vs control

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• Update analysis of L1000 genes in DGE

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