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Jz parse dagitty#21

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djinnome wants to merge 20 commits intoPayamDiba:masterPayamDiba/SERGIO:masterfrom PNNL-CompBio:jz-parse-dagittyPNNL-CompBio/SERGIO:jz-parse-dagittyCopy head branch name to clipboard

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Commits

Commits on Feb 16, 2023

• Adding all the R files related to conditional independence of a GRN.

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  NarmadhaMM

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  ec5bd8e

• Cleaned up the R scrips and files.

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  NarmadhaMM

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  3c0d833

Commits on Mar 10, 2023

• Added the R files for, 1) Test conditional independencies of Ecoli-GRN using existing data in SERGIO project (file name:GRN_Ecoli_ConditionalIndependence_sample size). 2) The HTML file with the out…

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  NarmadhaMM

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  f2c5354

Commits on Mar 23, 2023

• added the r files to create a GRN from an interaction file and conduct conditional independence tests.

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  NarmadhaMM

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  8c97f75

• R studio set up for git

  NarmadhaMM

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• Set up got for Rstudio

  NarmadhaMM

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• set up git for Rstudio and save all R scripts in the R project

  NarmadhaMM

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• Delete the old R project

  NarmadhaMM

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• Set up git in R stui and save all R scripts

  NarmadhaMM

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Commits on Mar 30, 2023

• Parse interactions

  djinnome

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• Conditional independence tests for simulated data (for all 9 cell types) (Rmd file and .R file named "GRN_Ecoli_ConditionalIndependence_samplesize".

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  NarmadhaMM

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Commits on Apr 6, 2023

• dagitt file

  djinnome

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• added noise by genes

  djinnome

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• getting Meenu's latest commits

  djinnome

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• Correcting incorrectly parsed the data on cell types.

  NarmadhaMM

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• daggity file associated with De-noised_100G_9T_300cPerT_4_DS1 data set

  djinnome

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• Correcting issue #6

  djinnome

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• Adding the notebook and the results from using DS1.daggity file. The results are exactly same as before. I think there is variability from cell types , and probably one data set may not be enough t…

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  NarmadhaMM

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Commits on Apr 13, 2023

• logit transformed simulated data

  djinnome

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• Merging Meenu's changes

  djinnome

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