theislab Goto Github PK

2015-grn-inference

Andrea Ocone’s GRN inference framework

2018_angelidis

Reproducibility repo accompanying Angelidis et al. "An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics"

2019_strunz

Reproducibility repo accompanying Strunz et al. "Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis". Nat Commun. 2020.

2020_inhibition_ltbetar-signalling

Reproducibility repo accompanying Thomas M Conlon, Mathias Heikenwälder et al. and Ali Yildirim "Inhibition of LTβR-signalling blocks epithelial apoptosis and activates Wnt-induced regeneration in lung"

2020_ips_lung_differentiation

Reproducibility repo accompanying Chaido Ori, Meshal Ansari, Ilias Angelidis, Fabian J. Theis, Herbert B. Schiller and Micha Drukker "Single cell trajectory mapping of human pluripotent stem cells differentiating towards lung and hepatocyte progenitors".

2020_mayr

This repo contains the analysis code describing the findings of Mayr_et_al

2021_aliluev_tritschler_gut_hfd

2021_prmt7_regulates_monocyte_extravasation

2022_bakhti_pancreas_syt13

2022_tritschler_pancreas_cross_species

anndata2ri

Convert between AnnData and SingleCellExperiment

archmap_admin

archmap_doc

astrocytes_reprogramming_analysis

atlas-feature-selection-benchmark

Code for benchmarking the effect of feature selection on scRNA-seq atlas construction and use

augurpy

A Python adaption of Augur to prioritize cell types in perturbation analysis.

autoencoderps

autogenes

bartseq

Software required for Bart-Seq technology – a cheap technology to analyze (single) cells using forward and reverse barcoding for target genes

bartseq-pipeline

Demultiplexing pipeline for BART-Seq

batchglm

Fit generalized linear models in python.

bindome

Assembling of biomolecule binding data (TF/RNA) from genomics databases for ML-downstream.

campa

Conditional Autoencoders for Multiplexed Pixel Analysis

campa_ana

Analysis of 4i data from CAMPA manuscript

cellrank

CellRank: dynamics from multi-view single-cell data

cellrank2_reproducibility

CellRank 2's reproducibility repository.

cellrank_notebooks

Tutorials and examples for CellRank.

cellrank_reproducibility

CellRank's reproducibility repository.

cellrank_reproducibility_preprint

Code to reproduce results from the CellRank preprint

chemcpa

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.