README.md

LNarch repository

Repository for Manuscript in revision with title:
Architectural principles of lymphoma-induced lymph node tissue remodeling

Contributors: Felix Czernilofsky, Lea Jopp-Saile, Anna Mathioudaki

Guide for code access

All code used in the manuscript can be accessed and cloned via the present repository

Data access and runs on manuscript data

Objects available in Zenodo. Raw data have been deposited in EGA.
Links will be made public upon acceptance.

Packages versions

Fastq preprocessing of scRNA-seq data

BD Rhapsody Docker image version 1.9 (https://hub.docker.com/u/bdgenomics)

Downstream scRNA-seq analysis:

Python v3.9
Scikit-learn v.1.3.2
R v.4.1.0 Seurat version v.4.3.0
Scanorama v.1.7.3
MAST v.1.22.0
ClusterProfiler v.4.6.3
DAseq v.1.0.0
NicheNet’s v.1.1.1
biomaRt v.2.28.0
Scriabin (installed from main in Oct2022)
pySCENIC v.0.11.1 & GRNboost2 from Arboreto package

Survival analysis

R v.4.1.0
maxstat package v.07.25
survminer v.0.4.9
survival v.3.1-12