STSM: Establishing a computational pipeline for myeloid-focused single-cell atlas curation

STSM CALL – Establishing a computational pipeline for myeloid-focused single-cell atlas curation - NOW OPEN

Host Institution: Technical University of Munich, Germany

Supervisor/Coordinator: Markus List

Instructors: Markus List, Florent Petitprez

Timeframe: 10th September to 16th September 2023

Attendees: On-site: 4x WG 1 members + 1x instructor

Purpose: Guided by current best-practices in single-cell RNA-sequencing (scRNA-seq) data analysis, we will put together a pipeline to integrate and re-annotate multi-study scRNA-seq data to curate disease-focused single-cell atlases with a focus in particular on myeloid cell annotation. As test cases, we will use single-cell datasets from breast cancer and inflammatory bowel disease (IBD) already selected by the WG 1 single-cell working groups; additional datasets could be possibly identified by instructors and participants prior to this STSM and be integrated in the analysis.

We plan to start from preprocessed scRNA-seq data (i.e. raw gene counts) and assemble a pipeline to perform: 1) data integration, 2) qualitative and quantitative assessment of data integration quality in terms of batch effect removal and conservation of biological information, and 3) cell-type annotation. If possible within the envisioned time frame, a preliminary deconvolution analysis will be performed on external bulk/spatial transcriptomics to assess the value of the curated atlases for scRNA-seq-informed deconvolution.

Tasks: It is our aim to assemble a computational pipeline for the curation of single-cell transcriptomic atlases from scRNA-seq data.

Selection Criteria: WG 1 members: Expertise in bioinformatics with a strong focus on scRNA-seq data analysis and integration. Preferably prior experience on in silico cell type deconvolution.


  • Availability from September 10th until September 16th, 2023.
  • Notebook / laptop and skills in R / Python to engage in data processing and application of in silico cell type deconvolution tools, plotting of results.
  • WG 1 members should have selected and uniformly preprocessed candidate data sets ready for analysis BEFORE the STSM.

Expected Outcome: Based on our work during the STSM, we will implement a computational pipeline for the curation of multi-study single-cell atlases from scRNA-seq data. The pipeline will be made available via GitHub to the Mye-InfoBank community to facilitate the curation of myeloid atlases in DACI performed by WG 1, with the support of WG 2 and WG 3.

Application Deadline: 2nd June 2023

Application form and further details


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