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2022_manatee_paper_analyses

Code implementing MANATEE used for the analyses in the associated paper.

3d_imc_publication

adnet

Repository for the analysis of the paper "Influence of node abundance on signaling network state and dynamics analyzed by mass cytometry"

airlab

airlab-web

AirLab is a laboratory management tool specialized in antibody-based research.

ansible-bbclient

Contains the ansible scripts to setup a bbclient

ansible-pgserver

The ansible playbook defining the postgres server used for vitoz sphere project.

bbrtools

R tools for the Bodenmiller lab

bbsnippets

This repository contains general examples, code snippets and guidelines.

bbwidgets

Interactive Widgets for the Jupyter Notebook

bc_ln_metastses

bc_rnaseq_integration

Code for the integration of the BCexh scRNA-seq dataset with published BC scRNA-seq datasets

bcexh_imc

To test workflowr

bcexh_scrnaseq

bcmet_publication_scripts

cafclassification

catalyst

Cytometry dATa anALYsis Tools

cellprofiler

An open-source application for biological image analysis

cellsighter

Code for the use of CellSighter in the Bodenmiller Lab

cisi-imc_publication

Scripts for CISI-IMC publication

cisi_imc

scripts for Tsuyoshi's CISI_IMC project

cookiecutter-jupyter

Bodenmiller Lab template for Python data analysis projects using Jupyter notebooks

core

cytofcompensation

Companion repository for the paper 'Compensation of signal spillover in suspension and imaging mass cytometry'

cytofkit

cytofkit: an integrated flow/mass cytometry data analysis pipeline

cytoimagelist

S4 class for storing multiple single- and multi-channel images in R.

cytomapper

R package for visualization of highly multiplexed imaging data

cytomapper_publication

See static website at https://bodenmillergroup.github.io/cytomapper_publication/

cytoviewer

An interactive multi-channel image viewer for R