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@GreshamLab The Gresham Lab at the NYU Center for Genomics and System Biology

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    35 repositories

    • CNV_Stability_without_selection_pressure

      Public
      Code associated with De et al. 2025
      Python
      •0•0•0•0•Updated Apr 5, 2026Apr 5, 2026

    • sc_self_supervised

      Public
      Self Supervised Tools for Single Cell Data
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 2, 2026Apr 2, 2026

    • vignettes

      Public
      A collection of vignettes describing common workflows in the Gresham lab
      Python
      •
      MIT License
      •0•1•0•0•Updated Mar 19, 2026Mar 19, 2026

    • IAV_intracellular_model

      Public
      Matlab scripts for the stochastic simulation of intracellular replication and population level modeling.
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated Mar 17, 2026Mar 17, 2026

    • jtb_2023_code

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Mar 5, 2026Mar 5, 2026

    • Quiescence_Candida_albicans

      Public
      Repository associated with Ozan Berk Imir's first author article on defining the growth phase of quiescence in Candida albicans
      MIT License
      •0•0•0•0•Updated Feb 26, 2026Feb 26, 2026

    • supirfactor-dynamical

      Public
      Build dynamical deep models for transcriptional biophysics
      Python
      •
      MIT License
      •0•1•0•0•Updated Feb 19, 2026Feb 19, 2026

    • SingleCell_cerevisiae

      Public
      Single cell RNA-sequencing on S. cerevisiae
      R
      •
      MIT License
      •0•1•0•0•Updated Jun 12, 2025Jun 12, 2025

    • local_arch_variants

      Public
      Code associated with eLife Chuong et al. 2025
      R
      •0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

    • CIVR_HRP_Day0

      Public
      Code for Forst et al., 2022
      R
      •0•0•1•0•Updated Aug 13, 2024Aug 13, 2024

    • adaptive_gene_expression

      Public
      A collection of code used in the analysis of "Multilevel gene expression changes in lineages containing adaptive copy number variants"
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 26, 2024Jun 26, 2024

    • cnv_sims_inference

      Public
      CNV simulation and inference of mutation rate and fitness effect
      HTML
      •
      MIT License
      •2•0•0•0•Updated Apr 17, 2024Apr 17, 2024

    • polyadenylation_cerevisiae

      Public
      Polyadenylation project on S. cerevisiae
      Shell
      •
      MIT License
      •0•2•0•0•Updated Mar 27, 2024Mar 27, 2024

    • vivaldi

      Public
      An R package for studying viral genetic diversity using vcf files
      R
      •
      Other
      •1•3•0•0•Updated Feb 15, 2024Feb 15, 2024

    • ferret-host-obesity

      Public
      R analyses associated with "Host obesity impacts genetic variation in influenza A viral populations"
      R
      •0•0•0•0•Updated Jul 12, 2023Jul 12, 2023

    • cnvflow

      Public
      workflow using CytoexploreR to analyze flow data from Cytek for CNV detection
      HTML
      •
      MIT License
      •0•0•0•0•Updated Nov 30, 2022Nov 30, 2022

    • heranca

      Public
      A small script for reducing false positive variant calls (VCFs) using lineage information
      Python
      •
      MIT License
      •1•0•0•0•Updated Sep 21, 2022Sep 21, 2022

    • rpy2deseq

      Public
      Python wrapper for DESeq2
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 5, 2022Sep 5, 2022

    • labtools

      Public
      useful R functions for data analysis
      R
      •1•1•1•0•Updated Feb 17, 2022Feb 17, 2022

    • tecantools

      Public
      For analysis of data that comes off of the Tecan Spark
      0•1•0•0•Updated Jan 28, 2022Jan 28, 2022

    • ggThemeScanpy

      Public
      ggplot2 themes that match scanpy default outputs
      R
      •
      MIT License
      •0•1•0•0•Updated May 2, 2021May 2, 2021

    • TitirPractice

      Public
      This is a practice repe to get Titir started with github.
      0•0•0•0•Updated Oct 27, 2020Oct 27, 2020

    • UGA4

      Public
      Analysis of UGA4 data
      HTML
      •0•0•0•0•Updated Oct 20, 2020Oct 20, 2020

    • CNV-detection-from-NGS

      Public
      Detecting copy number variation
      Shell
      •3•0•0•0•Updated Aug 7, 2020Aug 7, 2020

    • flowtools

      Public
      tools for analyzing flow cytometry data in the Gresham Lab
      R
      •
      MIT License
      •1•0•0•0•Updated Aug 4, 2020Aug 4, 2020

    • flow

      Public
      Scripts for processing flow cytometry and FACS data
      R
      •8•3•1•0•Updated Jul 14, 2020Jul 14, 2020

    • bartools

      Public
      tools for analyzing barseq data
      R
      •0•1•0•0•Updated Jul 14, 2020Jul 14, 2020

    • kallisto-yeast-analysis

      Public
      Scripts and Pipelines for Kallisto Analysis of Yeast Single-Cell Data
      Shell
      •
      MIT License
      •0•0•0•0•Updated Mar 30, 2020Mar 30, 2020

    • paracentral

      Public
      Small python script for sequence identification and extraction from contigs
      Python
      •0•0•0•0•Updated Mar 5, 2020Mar 5, 2020

    • mugio

      Public
      Inverted Repeat Junction identifier for use with ONT (MinION) sequencing.
      Python
      •
      MIT License
      •3•0•0•0•Updated Jan 30, 2020Jan 30, 2020
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