A weekly gathering of bioinformaticians at South Lake Union to discuss new methods, build public code, and foster community. Suggest topics in this repo's issues!
Tuesdays at 2 PM, Zoom
| Type | Description |
|---|---|
| Challenge | Following TidyTuesday (https://github.com/rfordatascience/tidytuesday), Advent of Code (https://adventofcode.com/2021), or tackling an open BIGslu GitHub issue, we work as a team to tackle coding challenges in R. Great for beginners! |
| Code review | Aimed at improving code and solving problems, these sessions provide formal review of member-submitted code. For details, see https://github.com/BIGslu/CodeReview |
| Discussion | These sessions provide informal discussion of current methods in bioinformatics. Members can submit topics such as R packages, journal articles, recent seminars, etc. Please review any posted literature prior to the session. |
| i4TB | Seminars and workshops in partnership with i4TB, https://trtc.uw.edu/education/i4tb-working-group |
| Workshop | Come ready to code-along or just watch these live-coded workshops! For details, see https://github.com/BIGslu/workshops |
| Date | Type | Topic |
|---|---|---|
| Jun 21 | Social | Join BIGslu along with i4TB and SEA-TRAC for our summer kick-off social! |
| Date | Type | Topic |
|---|---|---|
| May 31 | Challenge | Advent of Code, https://adventoIfcode.com/2021/ |
| May 17 | workshop | Custom ggplot themes and scales, https://github.com/BIGslu/BinningSingletons |
| May 10 | i4TB workshop | Dimensionality reduction and hierarchical clustering, Fergal Duffy https://github.com/fergaljd/i4TB/blob/main/i4TB-clustering-tutorial.Rmd |
| May 3 | Challenge | TidyTuesday https://github.com/rfordatascience/tidytuesday |
| Apr 19 | Challenge | BIGpicture::plot_gsea BIGslu/BIGpicture#6 |
| Apr 12 | i4TB seminar | An Integrative Approach to Supporting Data Science Research & Education at the U of Washington, Dr. Sarah Stone |
| Apr 5 | Challenge | Advent of Code, Day 4, https://adventoIfcode.com/2021/day/4 |
| Mar 29 | Discussion | Missing data. What do you do when you have missing data? Imputation vs subsetting? Statistical methods that allow missing? Etc. Helpful reading https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0494-3 |
| Mar 22 | Workshop | Create gene set analysis package with Basilin |
| Mar 15 | Discussion | Topics brainstorm |
| Mar 8 | Workshop | Linear models in R https://github.com/BIGslu/workshops/tree/main/2022.03.08_linear.model.workshop |
| Mar 1 | Discussion | TidyTuesday https://github.com/rfordatascience/tidytuesday |
| Feb 22 | Discussion | Rproject design and organization |
| Feb 8 | i4TB seminar | HealthAI at Amazon Web Services |
| Feb 1 | Code review | Elisabeth R. https://github.com/earosenthal/MMPhewas |
| Jan 25 | Workshop | Introduction to R and RStudio |
| Jan 18 | Discussion | ggplot: Sharing tips and tricks to customize your plots |
| Jan 11 | Workshop | i4TB: TCR analysis, Koshlan Mayer-Blackwell (Fred Hutch) |
| Dec 16 | Discussion | i4TB seminar from Dec 14 https://trtc.uw.edu/education/i4tb-working-group |
| Dec 9 | Discussion | Main reading: Linear models with weights https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551905/ Addtl background: limma https://academic.oup.com/nar/article/43/7/e47/2414268 https://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf |
| Dec 2 | Discussion | Controlling false discovery rate in genomics https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1716-1 |
| Nov 18 | Workshop | Introduction to how to contribute to BIGslu code and walk-through of completing a current GitHub issue and pull request |
| Nov 4 | Discussion | Working with SNP data in R, bigsnpr https://privefl.github.io/bigsnpr/articles/demo.html |
| Oct 28 | Workshop | Intro R in preparation for i4TB on Nov 9 https://github.com/BIGslu/workshops/tree/main/2021.10.28_introR.workshop |
| Oct 21 | Discussion | Topics brainstorm |
| Oct 14 | Code review | kimma::kmFit( ) https://github.com/BIGslu/kimma |
| Oct 7 | Discussion | Generalized additive models (GAM) in R https://petolau.github.io/Analyzing-double-seasonal-time-series-with-GAM-in-R/ |
| Sep 30 | Workshop | R packages: Documentation and examples https://github.com/BIGslu/workshops/tree/main/2021.09_R.package.workshop |
| Sep 23 | Workshop | R packages: Making a package with custom functions https://github.com/BIGslu/workshops/tree/main/2021.09_R.package.workshop |
| Sep 16 | Discussion | Partial Least Squares Regression for Generalized Linear Models in R, plsRglm https://cran.r-project.org/web/packages/plsRglm/index.html |
| Sep 9 | Code review | BIGpicture: Brainstorming useful bioinformatic plots and planning package development |
| Sep 2 | Code review | BIGpicture's first function: volcano plot https://github.com/BIGslu/CodeReview/tree/main/2021.08.24_volcano.plot |