New Gene Diagnostic Analysis#1461

Open

mpg19 wants to merge 194 commits intomasterfrom

ng-diagnostics-merge

Commits on Jan 11, 2024

choose initial new gene expression parameters for this project
rjuenemann
committed
Created analysis script for new gene diagnostic protein counts

Mia Grahn
authored and
Mia Grahn
committed

Commits on Jan 18, 2024

Merge branch 'master' into ng-diagnostics

Mia Grahn
authored and
Mia Grahn
committed

Commits on Feb 22, 2024

Initial new gene protein diagnostics plots

Mia Grahn
authored and
Mia Grahn
committed

Commits on Feb 29, 2024

update to the new_gene_protein_diagnostics.py script

Mia Grahn
authored and
Mia Grahn
committed

Commits on Mar 5, 2024

updated file to contain y vs x plots of PC comparisons for variants

Mia Grahn
authored and
Mia Grahn
committed

Commits on Mar 6, 2024

added another line of comparison to the x vs y variant comparison plots

Mia Grahn
authored and
Mia Grahn
committed

Commits on Mar 8, 2024

Created new analysis script for monitoring the counts for chosen proteins over a simulation's duration

Mia Grahn
authored and
Mia Grahn
committed
Changed file name

Mia Grahn
authored and
Mia Grahn
committed

Commits on Mar 21, 2024

Merge branch 'master' into ng-diagnostics

Mia Grahn
authored and
Mia Grahn
committed
Updated induction generation for sherlock sims

Mia Grahn
authored and
Mia Grahn
committed
Updated the gene_counts.py script to have the variant and seed numbers in the titles

Mia Grahn
authored and
Mia Grahn
committed

Commits on Apr 15, 2024

modular code style update to the code

Mia Grahn
authored and
Mia Grahn
committed
cleaned up the code a bit to have more clear messages and shorter lines of code

Mia Grahn
authored and
Mia Grahn
committed

Commits on Apr 16, 2024

added generation lines to the plots

Mia Grahn
authored and
Mia Grahn
committed
added generation lines to the plot

Mia Grahn
authored and
Mia Grahn
committed
WOP of gene_counts.py edit for generation designation lines

Mia Grahn
authored and
Mia Grahn
committed
fixed the generation lines on the plots

Mia Grahn
authored and
Mia Grahn
committed
added exceptions to the functions

Mia Grahn
authored and
Mia Grahn
committed

Commits on Apr 24, 2024

Commits on May 8, 2024

Updated the knowledge_base_raw.py file to have the new protein deg rate file.
mpg19
committed

Commits on May 9, 2024

Commits on May 15, 2024

Created gene_counts.py variant script initial draft.
mpg19
committed

Commits on May 16, 2024

Commits on May 22, 2024

Commits on May 24, 2024

Prepped for run in sherlock with a protein of interest
mpg19
committed

Commits on Jun 3, 2024

fixed translation.py for running sim with the exp then n end rule data.
mpg19
committed

Commits on Jun 5, 2024

Commits on Jun 6, 2024

Re-ran notebook file
mpg19
committed

Commits on Jun 14, 2024

Merge branch 'master' into ng-diagnostics
mpg19
committed

Commits on Aug 2, 2024

Merge branch 'master' into ng-diagnostics
mpg19
committed

Commits on Aug 3, 2024

Changed back to original version.
mpg19
committed

Commits on Aug 4, 2024

Commits on Aug 5, 2024

Commits on Aug 7, 2024

Updated with latest version of this file from Riley's branch.
mpg19
committed

Commits on Aug 8, 2024

Commits on Aug 10, 2024

Commits on Aug 20, 2024

Commits on Aug 22, 2024

Draft
mpg19
committed

Commits on Aug 27, 2024

Finished function code.
mpg19
committed

Commits on Aug 28, 2024

Commits on Dec 13, 2024

Editing gene counts scripts, work in progress.
mpg19
committed

Commits on Dec 22, 2024

Commits on Jan 7, 2025

Debugging check #1: checked that total_counts and free_counts are indexed correctly and in the same order.
mpg19
committed

Commits on Jan 10, 2025

Commits on Jan 14, 2025

Updated with new functions
mpg19
committed

Commits on Jan 19, 2025

Commits on Jan 28, 2025

Commits on Jan 29, 2025

Commits on Feb 9, 2025

Edited for final submission.
mpg19
committed

Commits on Feb 11, 2025

Commits on May 14, 2025

Edited file for more consistent averaging of the monomer counts data over cells when constructing validation output files.
mpg19
committed

Commits on Jul 10, 2025

minor edits.
mpg19
committed

Commits on Jul 28, 2025

Created changes for test debug run.
mpg19
committed

Commits on Jul 31, 2025

Editing output formatting.
mpg19
committed

Commits on Aug 5, 2025

Testing new for loop implementation.
mpg19
committed

Commits on Aug 7, 2025

Commits on Aug 8, 2025

Made plot titles cleaner.
mpg19
committed

Commits on Aug 12, 2025

Added optionality to include the table.
mpg19
committed