jaymgrayson Goto Github PK

biddyetalworkflow

This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.

breastcancercytof

modelling breast cancer cytof data with logic ODEs

capybara

Capybara: A computational tool to measure cell identity and fate transitions

carsten_cytof_code

cdcfluview

:mask: R package to Retrieve U.S. Flu Season Data from the CDC FluView Portal (WHO & ILINet)

celltag-classifier

celltagr

This repository contains the CellTag data analysis R package to support clone calling and lineage reconstruction.

clusterx

ClusterX: Fast clustering by automatic search and find of density peaks

code-to-analyze-flow-cytometry

codex

Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation. ############# ######## Non-public maven dependencies can be found here: https://1drv.ms/u/s!AmLT3VlVj2P_lf09PpFz6KxhKNboOw

cs-smaf

cytof_lsh

cytofkit

cytofkit: an integrated flow/mass cytometry data analysis pipeline

cytofkit2

cytometry-clustering-comparison

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

datasharing

The Leek group guide to data sharing

ds-examples

Data Science examples

faust

Full annotation using shape-constrained trees

getting_started_highdimflow

Some scripts to get you started with high dimensional flow symmetry data

gficf

An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization

immuneresistance

This resource provides the code developed in the study of Jerby-Arnon _et al. "Single-cell RNA-seq of melanoma ecosystems reveals sources of T cell exclusion linked to immunotherapy clinical outcomes".

jsom

lahav_imageanalysis_matlab_code

liu-virology

This is the R code we used in our Virology paper-"Unsupervised learning techniques reveal heterogeneity in memory CD8+ T cell differentiation following acute, chronic and latent infections"

macau

Bayesian Factorization with Side Information in C++ with Python wrapper

magic

MAGIC - imputation and de-noising single-cell RNA seq data sets

maker-pi-pico

mouse_2secl_paper

Data and scripts to generate figures used in Grayson et al-PLOS One

netsne

neur_721

Scripts for NEUR_721 class