Dear AgBioData Community:

Please see below an event on single-cell RNA-seq analysis that may be of interest to some of you.

Regards,

Marcela

*From: *Alex Clop alex.clop@cragenomica.es *Date: *Monday, April 27, 2026 at 9:30 AM *To: *faang-SingleCell@animalgenome.org faang-singlecell@animalgenome.org, Giuseppe-Antonio Saldi gas361@nyu.edu *Subject: *Seminar 18 May 2026 by G Saldi on analysis of scRNA-seq data

Dear colleagues,

Within the framework of the regular seminar series organized by the FAANG Single Cell Task Force, we are pleased to announce an upcoming online seminar by Dr Giuseppe A. Saldi (New York University Abu Dhabi, UAE).

Dr Saldi is a bioinformatician with extensive expertise in the analysis of single cell RNA sequencing (scRNA-seq) data and in the development of computational methodologies and tools for single cell transcriptomics

(*https://scholar.google.com/citations?user=o7hIBDwAAAAJ&hl=fr__;!!D9dNQww... https://scholar.google.com/citations?user=o7hIBDwAAAAJ&hl=fr__;!!D9dNQwwGXtA!TtXNLgMw37gAnM6lXo0OjOEgUVNTMnd-6QSm357Ny8ggn1vgEGZzMLGGZulOSlfgMPrDyEofuxImdvzfEtviiA$* ).

In this seminar, Dr Saldi will present an overview of the core analytical steps in scRNA-seq data analysis, with emphasis on the statistical and biological rationale underlying each step, from raw data pre-processing through differential gene expression (DGE) testing.

The focus will be on conceptual frameworks, assumptions, and common pitfalls associated with standard scRNA-seq workflows (e.g. quality control metrics, dimensionality reduction, and DGE design). Given the limited duration, the seminar will not provide an exhaustive comparison of alternative methods or software packages (e.g. detailed benchmarking of normalization strategies) but will instead aim to clarify why specific analytical steps are required and how analytical choices propagate downstream.

Date: Monday, May 18, 2026

Time: 17:00–19:40 (Central European Summer Time, CEST)

(Time conversions for other time zones are provided at the end of this email)

Format: Online

The session is structured to encourage active discussion, with dedicated question and discussion periods following each module.

Title: Analytical considerations in single cell RNA seq: from pre-processing to differential gene expression analysis

Program (~2 h 40 min):

• 17:00 – Welcome and introduction (~5 min)

• 17:05 – Background and high-level workflow overview (~15 min)

*Data structure, noise sources in scRNA-seq, and positioning of key analytical steps*

• 17:20 – Quality control considerations (~25 min)

*Cell and gene level QC metrics; mitochondrial transcript proportions; detection of doublets/multiplets; ambient RNA contamination and background correction*

• 17:45 – Discussion (~15 min)

• 18:00 – Break (15 min)

• 18:15 – Feature selection and dimensionality reduction (~30 min)

*Normalization and variance stabilization; log1p transformation; identification of highly variable genes (HVGs); principal component analysis (PCA)*

• 18:45 – Discussion (~15 min)

• 19:00 – Differential gene expression (DGE) analysis (~25 min)

*DGE strategies in single cell contexts; pseudo replication; statistical power; appropriate experimental and model design*

• 19:25 – Discussion (~15 min)

• 19:40 – Closing remarks

Access: The seminar will be held online via Teams: *Joseph FAANG SC | Meeting-Join | Microsoft Teams https://teams.microsoft.com/meet/348312092317295?p=jgru5YQSAWnvSG00a2*

Time zone conversions:

• CEST (Barcelona): 17:00–19:40

• New York (EDT): 11:00–13:40

• Los Angeles (PDT): 08:00–10:40

• Beijing (CST): 23:00–01:40 (+1 day)

• Tokyo (JST): 00:00–02:40 (+1 day)

• Sydney (AEST): 01:00–03:40 (+1 day)

Note that you may have received, in parallel, an automatic email from Teams informing about this seminar, as a result of the schedule of this meeting in the Teams calendar.

With kind regards,

Alex Clop¹ and Christopher K. Tuggle²

¹ Centre for Research in Agricultural Genomics (CRAG)

Campus UAB

08193 Cerdanyola del Vallès

Catalonia, Spain

*https://www.cragenomica.es https://www.cragenomica.es/*

² Iowa State University — Department of Animal Science

C. F. Curtiss Distinguished Professor in Agriculture and Life Sciences

806 Stange Road, 2255 Kildee Hall

Ames, IA 50011, USA

Email: *cktuggle@iastate.edu cktuggle@iastate.edu*

Phone: +1 515 294 4252

FAX 515-294-2401

*http://www.ans.iastate.edu/people/christopher-tuggle http://www.ans.iastate.edu/people/christopher-tuggle*