Khalil Lab

Pinned Repositories

coop-synTF-model
Model and analysis code for synthetic TF cooperativity project
Language:MATLAB0 5 00
coop-TF-custom-analyses
One-off analyses and figures for Bragdon et. al. 2022.
Language:R00
coop-TF-specificity
Language:Jupyter Notebook00
DDR-eVOLVER-model
Scripts used to execute DDR eVOLVER experiments and ecology simulations
Language:Jupyter Notebook1 5 00
ePACE-Nme2Cas9-analysis
Scripts used for analysis in the Nme2Cas9 evolution project.
Language:Jupyter Notebook0 4 00
evolver-analyze
MATLAB package for basic analysis of raw eVOLVER data files generated as in Wong et al 2018.
Language:MATLAB10
HSF1-heatshock-model
Titration Model of Hsf1 Dynamics
Language:MATLAB0 5 00
m6a-model
Gillespie model for m6a spreading by synthetic read-write modules
Language:MATLAB0 5 00
ncov-dca
Direct Coupling Analysis of SARS-CoV-2 genomes
Language:Python21
prion-bet-hedging-model
Language:MATLAB00

Khalil Lab's Repositories

khalillab/ncov-dca
Direct Coupling Analysis of SARS-CoV-2 genomes
Language:Python21
khalillab/DDR-eVOLVER-model
Scripts used to execute DDR eVOLVER experiments and ecology simulations
Language:Jupyter Notebook1 5 00
khalillab/evolver-analyze
MATLAB package for basic analysis of raw eVOLVER data files generated as in Wong et al 2018.
Language:MATLAB10
khalillab/coop-synTF-model
Model and analysis code for synthetic TF cooperativity project
Language:MATLAB0 5 00
khalillab/coop-TF-custom-analyses
One-off analyses and figures for Bragdon et. al. 2022.
Language:R00
khalillab/coop-TF-specificity
Language:Jupyter Notebook00
khalillab/ePACE-Nme2Cas9-analysis
Scripts used for analysis in the Nme2Cas9 evolution project.
Language:Jupyter Notebook0 4 00
khalillab/HSF1-heatshock-model
Titration Model of Hsf1 Dynamics
Language:MATLAB0 5 00
khalillab/m6a-model
Gillespie model for m6a spreading by synthetic read-write modules
Language:MATLAB0 5 00
khalillab/primer-designer-cloning
Language:Python00
khalillab/prion-bet-hedging-model
Language:MATLAB00
khalillab/prion-state-model
Language:MATLAB0 4 00
khalillab/programming-workshops
Accessory files and materials for Khalil Lab programming workshops.
0 5 00
khalillab/coop-TF-chipseq
ChIP-seq analysis pipeline used in Bragdon et. al. 2022.
Language:R
khalillab/coop-TF-rna-vs-chipseq
Workflow used to compare RNA-seq and ChIP-seq data for Bragdon et. al. 2022.
Language:Python
khalillab/coop-TF-rnaseq
RNA-seq analysis pipeline used in Bragdon et. al. 2022.
Language:R
khalillab/evolver-docs
Gitbook documentation for eVOLVER
2
khalillab/evolver-electron
temporary, separate from FYNCH distribution
Language:JavaScript
khalillab/guideseq
Analysis pipeline for the GUIDE-seq assay.
Language:Python
khalillab/large-cage
Agent-based modelling for the spread of gene drives and anti-drives in a large cage setting
Language:Python4 0
khalillab/synZiFTR-analyses
search for sequences in genome