Info about NIH-IRP Single Cell Users Group events
We will be posting information about upcoming users group events and other information here. For Single Cell Genomics SIG organized or cross-listed events, please visit this site.
Location and Speaker TBA
WebEx Link: 172 241 0782
Meeting PW: jjM4nAT3e@4
Audio-only Call-in #: 1-650-479-3207 (Access code: 172 241 0782)
Recording of preserntation here: Recording
Recording of presentation here: Recording
Recording of presentation here: Recording
Topic: “Seurat v3 Integration Walkthrough”
Slides now available here: Slides as .pptx
Rmarkdown now available here: Rmarkdown
Note for Stefan on Rmarkdown: “Still required are the datasets from 10X and a GTF human annotation file, which you can get from ENSEMBL. If you put data and annotation into subdirectories called “data” and ref of some local base directory and enter the name of your base directory into the R markdown, things should work.”
2x20min Presentations: Chrisine Hollander (Li Yang’s Lab - NCI) & Kathryn McClelland (Brian Oliver’s Lab - NIDDK)
Topic: “Single Nuclei”
Discussion Leader: Kaya Matson (Levine Lab, NINDS)
Slides now available here: PDF of Slides
Please give us feedback about this workshop: Survey Link (via Google Forms)
Date: March 6th, 2019
· Basic utility / concepts of scRNA-Seq
· Understanding “primary” analysis outputs, challenges
· Data pre-processing steps: filtering, dimensionality reduction, etc
· Clustering and interpretation of clusters
· High dimension dataset visualization background
Workshop coordinator: Assaf Magen and Stefan Cordes
Slide now availalbe here: PDF of Slides
Additional materials available here:
R Markdown
HTML of R Markdown
ScanPy Analysis of Mouse Hematopoietic Cell Atlas Data
convenience utilities
Date: April 24th, 2019
· Workflow for multi-dataset alignment and analysis, with example dataset and R-markdown code
· Basic trajectory analysis
Workshop coordinator: Stefan Cordes and Assaf Magen
2x20min Presentation: Art Shaffer (Staudt Lab - NCI) & Shouguo Gao (Young Lab - NHLBI)
Discussion Session: “Trajectory Analysis: Orienting single cell along a right path”
NIH Single Cell Workshop - Single Cell Sorting for Plate-Based Genomic Assays
2x20min Presentation: Erica Bresciani (Liu Lab - NHGRI) & Sharvani Mahadevaraju / Justin Fear (Oliver Lab - NIDDK)
2x20min Presentation: Jamie Diemer (Liu Lab - NHGRI) & Jessica Kang (Bodine Lab - NHGRI)
More Info Here: https://iig.niaid.nih.gov
And Here: https://nih-irp-singlecell.github.io/SingleCellGenomics-SIG/
Discussion Group - “Contamination”
(Bld35A, GG607 - Bottom floor meeting room closest to parking deck)
10X Genomics Mini Symposium
(Bld35A, Seminar Room 610)
Partek Seminar: Single Cell Analysis with Partek Flow
Presenter: Dr. Cherry Ignacio
Event Description: Join us for this seminar to learn how the intuitive graphical user interface and interactive tools of Partek Flow software can simplify your scRNA-Seq analysis. We will demonstrate how to analyze a scRNA-Seq data set with multiple biological replicates and detect genes that are differentially expressed between cell populations across sample groups.
(Bld35A, Seminar Room 620)
(Bld 40 Sem Rm): 2x20 Presentations – Elisabeth Heuston (Bodine Lab, NHGRI) & Stefania Dell’Orso (Office of Science & Technology, NIAMS)
Discussion Group - “Sample Prep”
(Bld35A, 1G600 - Orange Skybox in Atrium)
PDF of slides: SC-UsersGroup/2017-10-18_scUG Discussion_2.pdf
(Bld 40 Sem Rm): 2x20 Presentations – Barrett Lab (NHLBI) & Luigi Alvarado (Larochelle Lab, NHLBI)
Discussion Group ”Comparing cells across conditions”
2x20min Presentation: Beth Psaila & Eli Boritz
Intro Meeting, Lightning Talks, and Coffee Social
Join the Single Cell Genomics SIG listserv.
For joining the Single Cell Genomics SIG listserv:
This will allow you to subscribe to this listserv and you should be able to see some of the message archives on there as well.
If you would like to present or lead a discussion group, please contact one of us on the organizing team (you can find our email addresses on NIH global).
Jamie Diemer (NHGRI), Ben Voisin (NIAMS), Erica Bresciani (NHGRI), Chen Yao (NIAMS), Stefan Cordes (NHLBI), Lingling Miao (NIAMS), Supreet Agarwal (NCI), Byunghyun Kang (NIAID), Mike Kelly (NCI)