The Gresham Lab at the NYU Center for Genomics and System Biology
Github Organization for all Gresham Lab Code
NYC
Pinned Repositories
bartools
tools for analyzing barseq data
flow
Scripts for processing flow cytometry and FACS data
flowtools
tools for analyzing flow cytometry data in the Gresham Lab
labtools
useful R functions for data analysis
polyadenylation_cerevisiae
Polyadenylation project on S. cerevisiae
RATE_seq
RNAseq
The Gresham Lab RNAseq pipeline
trumiseq
Analysis scripts for TrUMIseq adaptors
vignettes
A collection of vignettes describing common workflows in the Gresham lab
vivaldi
An R package for studying viral genetic diversity using vcf files
The Gresham Lab at the NYU Center for Genomics and System Biology's Repositories
GreshamLab/vivaldi
An R package for studying viral genetic diversity using vcf files
GreshamLab/flow
Scripts for processing flow cytometry and FACS data
GreshamLab/bartools
tools for analyzing barseq data
GreshamLab/ggThemeScanpy
ggplot2 themes that match scanpy default outputs
GreshamLab/jtb_2023_code
GreshamLab/labtools
useful R functions for data analysis
GreshamLab/polyadenylation_cerevisiae
Polyadenylation project on S. cerevisiae
GreshamLab/SingleCell_cerevisiae
Single cell RNA-sequencing on S. cerevisiae
GreshamLab/supirfactor-dynamical
Build dynamical deep models for transcriptional biophysics
GreshamLab/vignettes
A collection of vignettes describing common workflows in the Gresham lab
GreshamLab/cnvflow
workflow using CytoexploreR to analyze flow data from Cytek for CNV detection
GreshamLab/flowtools
tools for analyzing flow cytometry data in the Gresham Lab
GreshamLab/RATE_seq
GreshamLab/RNAseq
The Gresham Lab RNAseq pipeline
GreshamLab/tecantools
For analysis of data that comes off of the Tecan Spark
GreshamLab/trumiseq
Analysis scripts for TrUMIseq adaptors
GreshamLab/adaptive_gene_expression
A collection of code used in the analysis of "Multilevel gene expression changes in lineages containing adaptive copy number variants"
GreshamLab/ASsc-RNA-seq
Allele Specific scRNAseq
GreshamLab/CIVR_HRP_Day0
Code for Forst et al., 2022
GreshamLab/CNV-detection-from-NGS
Detecting copy number variation
GreshamLab/ferret-host-obesity
R analyses associated with "Host obesity impacts genetic variation in influenza A viral populations"
GreshamLab/heranca
A small script for reducing false positive variant calls (VCFs) using lineage information
GreshamLab/kallisto-yeast-analysis
Scripts and Pipelines for Kallisto Analysis of Yeast Single-Cell Data
GreshamLab/mugio
Inverted Repeat Junction identifier for use with ONT (MinION) sequencing.
GreshamLab/paracentral
Small python script for sequence identification and extraction from contigs
GreshamLab/rpy2deseq
Python wrapper for DESeq2
GreshamLab/Santana-et-al-2019
Code used for all analyses in Santana et al., 2019
GreshamLab/sc_self_supervised
Self Supervised Tools for Single Cell Data
GreshamLab/TitirPractice
This is a practice repe to get Titir started with github.
GreshamLab/UGA4
Analysis of UGA4 data