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    • Code associated with De et al. 2025
      Python
      0000Updated Apr 5, 2026Apr 5, 2026
    • Self Supervised Tools for Single Cell Data
      Python
      MIT License
      0000Updated Apr 2, 2026Apr 2, 2026
    • vignettes

      Public
      A collection of vignettes describing common workflows in the Gresham lab
      Python
      MIT License
      0100Updated Mar 19, 2026Mar 19, 2026
    • Matlab scripts for the stochastic simulation of intracellular replication and population level modeling.
      MATLAB
      MIT License
      0000Updated Mar 17, 2026Mar 17, 2026
    • Python
      MIT License
      0200Updated Mar 5, 2026Mar 5, 2026
    • Repository associated with Ozan Berk Imir's first author article on defining the growth phase of quiescence in Candida albicans
      MIT License
      0000Updated Feb 26, 2026Feb 26, 2026
    • Build dynamical deep models for transcriptional biophysics
      Python
      MIT License
      0100Updated Feb 19, 2026Feb 19, 2026
    • Single cell RNA-sequencing on S. cerevisiae
      R
      MIT License
      0100Updated Jun 12, 2025Jun 12, 2025
    • Code associated with eLife Chuong et al. 2025
      R
      0000Updated Mar 4, 2025Mar 4, 2025
    • Code for Forst et al., 2022
      R
      0010Updated Aug 13, 2024Aug 13, 2024
    • A collection of code used in the analysis of "Multilevel gene expression changes in lineages containing adaptive copy number variants"
      Python
      MIT License
      1000Updated Jun 26, 2024Jun 26, 2024
    • CNV simulation and inference of mutation rate and fitness effect
      HTML
      MIT License
      2000Updated Apr 17, 2024Apr 17, 2024
    • Polyadenylation project on S. cerevisiae
      Shell
      MIT License
      0200Updated Mar 27, 2024Mar 27, 2024
    • vivaldi

      Public
      An R package for studying viral genetic diversity using vcf files
      R
      Other
      1300Updated Feb 15, 2024Feb 15, 2024
    • R analyses associated with "Host obesity impacts genetic variation in influenza A viral populations"
      R
      0000Updated Jul 12, 2023Jul 12, 2023
    • cnvflow

      Public
      workflow using CytoexploreR to analyze flow data from Cytek for CNV detection
      HTML
      MIT License
      0000Updated Nov 30, 2022Nov 30, 2022
    • heranca

      Public
      A small script for reducing false positive variant calls (VCFs) using lineage information
      Python
      MIT License
      1000Updated Sep 21, 2022Sep 21, 2022
    • rpy2deseq

      Public
      Python wrapper for DESeq2
      Python
      MIT License
      0000Updated Sep 5, 2022Sep 5, 2022
    • labtools

      Public
      useful R functions for data analysis
      R
      1110Updated Feb 17, 2022Feb 17, 2022
    • For analysis of data that comes off of the Tecan Spark
      0100Updated Jan 28, 2022Jan 28, 2022
    • ggplot2 themes that match scanpy default outputs
      R
      MIT License
      0100Updated May 2, 2021May 2, 2021
    • This is a practice repe to get Titir started with github.
      0000Updated Oct 27, 2020Oct 27, 2020
    • UGA4

      Public
      Analysis of UGA4 data
      HTML
      0000Updated Oct 20, 2020Oct 20, 2020
    • Detecting copy number variation
      Shell
      3000Updated Aug 7, 2020Aug 7, 2020
    • flowtools

      Public
      tools for analyzing flow cytometry data in the Gresham Lab
      R
      MIT License
      1000Updated Aug 4, 2020Aug 4, 2020
    • flow

      Public
      Scripts for processing flow cytometry and FACS data
      R
      8310Updated Jul 14, 2020Jul 14, 2020
    • bartools

      Public
      tools for analyzing barseq data
      R
      0100Updated Jul 14, 2020Jul 14, 2020
    • Scripts and Pipelines for Kallisto Analysis of Yeast Single-Cell Data
      Shell
      MIT License
      0000Updated Mar 30, 2020Mar 30, 2020
    • Small python script for sequence identification and extraction from contigs
      Python
      0000Updated Mar 5, 2020Mar 5, 2020
    • mugio

      Public
      Inverted Repeat Junction identifier for use with ONT (MinION) sequencing.
      Python
      MIT License
      3000Updated Jan 30, 2020Jan 30, 2020
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