| A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | AA | AB | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | LIBD rstats club | http://research.libd.org/rstatsclub/#.XpB1SNNKiL8 | Twitter/X + Bluesky | LIBD rstats club (@LIBDrstats) / X | https://bsky.app/profile/libdrstats.bsky.social | |||||||||||||||||||||||
2 | Code of conduct | Announcements and reminders | https://groups.google.com/d/forum/libd-rstats-club | Suggest topics | https://forms.gle/mREfqxbaikh7FAhf6 | |||||||||||||||||||||||
3 | Date | Presenter | Recording Link | Software / R packages | Topic | Difficulty level: beginner, intermediate, advanced | Slides / material | Twitter / X | Bluesky | Code | Notes by you | |||||||||||||||||
4 | TBD | David Zhang | poetry, cookiecutter | Developing python packages; an R users perspective | Advanced | https://py-pkgs.org/ | ||||||||||||||||||||||
5 | TBD | Geo Pertea | rwrap | Explore rwrap and rpy2 from https://twitter.com/kpj_py/status/1485650880187805698?s=21 | Intermediate | |||||||||||||||||||||||
6 | TBD | Leonardo Collado Torres | Writing blog posts | Beginner | ||||||||||||||||||||||||
7 | TBD | Geo Pertea | qs, fst | qs: faster save/load of R objects; fst: fast dataframe save/load, with slice loading option | Beginner | |||||||||||||||||||||||
8 | TBD | Geo Pertea | conda, python, R | setting up isolated conda enviroments | Advanced | |||||||||||||||||||||||
9 | TBD | Hedia Tnani | SQL, R, & dplyr | Intermediate | ||||||||||||||||||||||||
10 | TBD | Hedia Tnani | How to make an R package from an Rmarkdown | Advanced | How to make an R package from an Rmarkdown | |||||||||||||||||||||||
11 | TBD | |||||||||||||||||||||||||||
12 | TBD | |||||||||||||||||||||||||||
13 | ||||||||||||||||||||||||||||
14 | 2025-01-17 | |||||||||||||||||||||||||||
15 | 2025-01-10 | |||||||||||||||||||||||||||
16 | 2025-01-03 | (Leo PTO) | ||||||||||||||||||||||||||
17 | 2024-12-27 | CANCELLED (LIBD winter holiday) | ||||||||||||||||||||||||||
18 | 2024-12-20 | (Leo PTO) | ||||||||||||||||||||||||||
19 | 2024-12-13 | |||||||||||||||||||||||||||
20 | 2024-12-06 | (Leo on a conf) | ||||||||||||||||||||||||||
21 | 2024-11-29 | CANCELLED (Thanksgiving break) | ||||||||||||||||||||||||||
22 | 2024-11-22 | Nick | ENACT (https://doi.org/10.1101/2024.10.17.618905) | The ENACT pipeline for Visium HD analysis | ||||||||||||||||||||||||
23 | 2024-11-15 | Leonardo Collado Torres | https://youtu.be/hclxkkp-V_I | Bluesky | Live exploration of latest #RStats news on Bluesky | Beginner | https://www.one-tab.com/page/3P4xlfWzRs2tq3K9oPIx4g | |||||||||||||||||||||
24 | 2024-11-08 | CANCELLED | ||||||||||||||||||||||||||
25 | 2024-11-01 | Manisha Barse | [2024-11-01] An overview of SpaceRanger summary metrics | SpaceRanger | SpaceRanger metrics_summary.csv files and how to explore them | https://speakerdeck.com/manishabarse/exploring-spaceranger-summary-metrics | https://x.com/LIBDrstats/status/1854544951750619477 | https://bsky.app/profile/libdrstats.bsky.social/post/3laeks3fjkg23 | ||||||||||||||||||||
26 | 2024-10-18 | Leonardo Collado Torres, Nick, Louise | [2024-10-18] Debugging Bioconductor packages under review (visiumStitched and DeconvoBuddies) | visiumStitched, DeconvoBuddies, Bioconductor's Single Package Builder (SBP) | R/Bioconductor package development troubleshooting with our current packages under review | Advanced | https://github.com/Bioconductor/Contributions/issues/3501 | https://twitter.com/lcolladotor/status/1847290897483858308 | https://bsky.app/profile/lcolladotor.bsky.social/post/3l6sa6hx23m2z | https://github.com/Bioconductor/Contributions/issues/3503 | ||||||||||||||||||
27 | 2024-10-11 | Cynthia Soto | [2024-10-11] An overview of the CellRanger-ARC Pipeline Analysis | An overview of the CellRanger-ARC Pipeline Analysis | Cell RangerARC, Cell RangerARC-reanalyze, Cell Ranger-count and Cell Ranger-atac | Intermediate | https://www.10xgenomics.com/support/software/cell-ranger-arc/latest | https://bsky.app/profile/cynthiasc.bsky.social/post/3lahmijsy5t2h | For recovery cells when Cell RangerARC standard pipeline fails | |||||||||||||||||||
28 | 2024-09-27 | Leonardo Collado Torres | [2024-09-27] Multicellular Factor Analysis (MFA/MOFA) overview | MOFA, MOFA2, MOFAcellulaR, LIANA+ | Multicellular Factor Analysis overview | Beginner | 2024-09-27 Multicellular Factor Analysis overview | https://twitter.com/lcolladotor/status/1839700447822491820 | https://bsky.app/profile/lcolladotor.bsky.social/post/3l55ko75xys27 | |||||||||||||||||||
29 | 2024-08-09 | Cynthia Soto | [2024-08-09] GLM-PCA overview | glmpca | GLM-PCA overview | Intermediate | Slides: https://speakerdeck.com/cyntsc/glm-pca-overview and Paper: https://doi.org/10.1186/s13059-019-1861-6 | https://bsky.app/profile/cynthiasc.bsky.social/post/3lb3kwf2qd22z | Feature selection and dimension reduction for single-cell RNA-seq based on multinomial model | |||||||||||||||||||
30 | 2024-08-02 | KJ Benjamin | [2024-08-02] An overview on colocalization analyses | coloc, fastENLOC, DAP-G, SuSiE | colocalization | Intermediate | rstats-colocalization | coloc_examples.ipynb | ||||||||||||||||||||
31 | 2024-07-19 | KJ Benjamin | [2023-07-19] A quick overview of nano and rapids from nvidia - YouTube | nano, rapids | A quick overview of nano and rapids from nvidia | Beginner | GNU nano and RAPIDS.ai | |||||||||||||||||||||
32 | 2024-07-12 | Leonardo Collado Torres | (was considered not useful) | spatialLIBD, devtools, usethis | Working through some spatialLIBD bug reports | Advanced | ||||||||||||||||||||||
33 | 2024-07-05 | CANCELLED (LIBD extended holiday for 4th of July) | ||||||||||||||||||||||||||
34 | 2024-06-28 | Daianna Gonzalez-Padilla | [2024-06-28] Daianna Gonzalez-Padilla: my 2 years at LIBD - YouTube | none | Summary of remote work for LIBD since LIBD Summer Internship in 2022 | Beginner | My_2years_at_the_LIBD | https://twitter.com/daianna_glez/status/1810765027990983038 | ||||||||||||||||||||
35 | 2024-05-31 | Cynthia Soto (Leo PTO) | [2024-05-31] How I am using spatialLIBD with new features - YouTube | spatialLIBD app v17+ user experience | How I am using spatialLIBD with new features | Beginner | ||||||||||||||||||||||
36 | 2024-05-24 | Video recording | Private link | GENCODE, recount3 | Tamara Perteghella: GENCODE—Uncovering and cataloguing the human transcriptome complexity Ana Viñuela: Direct long-read RNA sequencing uncovers functional variation affecting transcript production and RNA modification | |||||||||||||||||||||||
37 | 2024-05-17 | Video recording | Private link | brainSCOPE, FICTURE | Prashant Emani: PsychENCODE integrative analysis—Single-cell genomics and regulatory networks for 388 human brains Yichen Si: FICTURE—Segmentation-free factor analysis for sub-micron resolution spatial transcriptomics | https://github.com/seqscope/ficture | ||||||||||||||||||||||
38 | 2024-05-03 | Louise Huuki-Myers | [2024-05-03] How to use DeconvoBuddies for deconvolution of bulk RNA-seq data | DeconvoBuddies | How to use DeconvoBuddies for deconvolution of bulk RNA-seq data | Intermediate | https://speakerdeck.com/lahuuki/benchmarking-deconvolution-methods-in-the-human-brain | https://x.com/lahuuki/status/1790835212353683539 | ||||||||||||||||||||
39 | 2024-04-26 | Nick Eagles | [2024-04-26] spatialLIBD multi-gene plotting and Shiny updates - YouTube | spatialLIBD, Shiny | spatialLIBD multi-gene plotting and Shiny updates | Beginner | http://research.libd.org/spatialLIBD/articles/multi_gene_plots.html | https://twitter.com/LIBDrstats/status/1790832408750903781 | https://bsky.app/profile/libdrstats.bsky.social/post/3kskhsvutgv2m | |||||||||||||||||||
40 | 2024-04-19 | Cynthia Soto | [2024-04-19] Joint RNA and ATAC from 10x scMultiomic datasets part 3 - YouTube | Seurat, Signac Part. III | Joint RNA and ATAC from 10x scMultiomic datasets | Intermediate | https://github.com/cyntsc/RStatClub_Seurat_Signac/blob/main/Supplemental_material/RStatClub.3_2024_SeuratClustering.pdf | https://github.com/cyntsc/RStatClub_Seurat_Signac/blob/5e325042d76bbe6b56669ee8e8545e01c4122add/code/03_Joint_step2.R | This is the presentation 3 of 3 to analize scMultiome data with Seurat and Signac. | |||||||||||||||||||
41 | 2024-04-12 | Leonardo Collado Torres | [2024-04-12] A user perspective on using iSEE interactive websites | iSEE | A user perspective on using iSEE interactive websites | Beginner | 2024-04-12 A user perspective on using iSEE interactive websites | https://twitter.com/lcolladotor/status/1779213376494727352 | https://bsky.app/profile/lcolladotor.bsky.social/post/3kpztuxkxxe2h | |||||||||||||||||||
42 | 2024-04-05 | Leonardo Collado Torres | [2024-04-05] Diving into the new JHPCE documentation website and updating JHPCE SLURM configuration | JHPCE, ~/.bashrc, ~/.slurm/defaults, documentation website | Diving into the new JHPCE documentation website and updating JHPCE SLURM configuration files | Intermediate | https://jhpce.jhu.edu/, https://lcolladotor.github.io/bioc_team_ds/config-files.html#jhpce-files | https://twitter.com/lcolladotor/status/1779209787340681678 | https://bsky.app/profile/lcolladotor.bsky.social/post/3kpzt6vyqxw2c | |||||||||||||||||||
43 | 2024-03-29 | CANCELLED -- think of attending https://satijalab.org/scgd24/ instead | ||||||||||||||||||||||||||
44 | 2024-03-22 | Cynthia Soto | [2024-03-22] MultiOmics with Seurat + Signac (DimRed and Clustering) part 2 | Seurat, Signac Part. II | MultiOmics with Seurat + Signac (DimRed and Clustering) | Intermediate | https://github.com/cyntsc/RStatClub_Seurat_Signac/blob/551c0b71f816910e45336dbfc5b9f1de7f024b2c/Supplemental_material/RStatClub.2_2024_SeuratClustering.pdf | https://github.com/cyntsc/RStatClub_Seurat_Signac/blob/5e325042d76bbe6b56669ee8e8545e01c4122add/code/02_Clustering.R | This is the presentation 2 of 3 to analize scMultiome data with Seurat and Signac. | |||||||||||||||||||
45 | 2024-03-15 | Leonardo Collado Torres (guest Stephanie Page) | [2024-03-15] winOS setup (shorter version) - YouTube | RStudio, WinSCP, Git Bash (for Windows), Notepad++ | JHPCE + RStudio + GitHub setup (Windows version) | Beginner | 2020-04-23 JHPCE Windows Setup | https://twitter.com/lcolladotor/status/1770278288063070319 | https://bsky.app/profile/lcolladotor.bsky.social/post/3ko3tuvfg3t2b | |||||||||||||||||||
46 | 2024-03-08 | Leonardo Collado Torres (guest Svitlana Bach) | [2024-03-08] macOS setup (shorter version) - YouTube | JHPCE, macOS, RStudio, Cyberduck, ssh keys | JHPCE RStudio setup (macOS version) | Beginner | https://gist.github.com/lcolladotor/3b1063db30a206835ee7e086c8f037ee | https://twitter.com/lcolladotor/status/1770274824243294256 | https://bsky.app/profile/lcolladotor.bsky.social/post/3ko3t37noa72g | |||||||||||||||||||
47 | 2024-03-01 | Leonardo Collado Torres | [2024-03-01] ggplot2 v3.5.0 updates overview part 2 - YouTube | ggplot2 | ggplot2 v3.5.0 upgrades part 2 | Advanced | https://www.tidyverse.org/tags/ggplot2-3-5-0/ | https://twitter.com/lcolladotor/status/1763796222832148874 | https://bsky.app/profile/lcolladotor.bsky.social/post/3kmounta5452k | |||||||||||||||||||
48 | 2024-02-23 | Leonardo Collado Torres | [2024-02-23] ggplot2 v3.5.0 updates overview - YouTube | ggplot2 | ggplot2 v3.5.0 upgrades | Advanced | https://www.tidyverse.org/blog/2024/02/ggplot2-3-5-0/ | https://twitter.com/lcolladotor/status/1761084492058607897 | https://bsky.app/profile/lcolladotor.bsky.social/post/3km42j3zm4l2p | |||||||||||||||||||
49 | 2024-02-09 | Cynthia Soto | [2024-02-09] MultiOmics with Seurat + Signac (Ambient RNA and preprocessing GEX and ATAC) - YouTube | Seurat, Signac Part I | MultiOmics with Seurat + Signac (Ambient RNA and preprocessing GEX and ATAC) | Intermediate | https://github.com/cyntsc/RStatClub_Seurat_Signac | https://github.com/cyntsc/RStatClub_Seurat_Signac/blob/5e325042d76bbe6b56669ee8e8545e01c4122add/code/01_GEX_ATAC_preprocessing2.R | This is the presentation 1 of 3 to analize scMultiome data with Seurat and Signac. | |||||||||||||||||||
50 | 2024-02-02 | Hedia Tnani + Geo Pertea | [2024-02-02] Differential Transcript Expression (DTE) methods - YouTube | limma, edgeR, tximport | Differential Transcript Expression (DTE) methods | Intermediate | Differential Transcript Expression methods | |||||||||||||||||||||
51 | 2024-01-26 | Leonardo Collado Torres | [2024-01-26] RStudio setup, projects, and shortcuts - YouTube | RStudio | RStudio setup, projects, and shortcuts | Beginner | 2024-01-26 RStudio setup, projects, and shortcuts | https://twitter.com/lcolladotor/status/1758623916073910425 | https://bsky.app/profile/lcolladotor.bsky.social/post/3klky43v43k2k | |||||||||||||||||||
52 | 2023-12-15 | Sean+Nick+Hedia | [2023-12-15] Key Nextflow concepts and building a pipeline from existing scripts - YouTube | Nextflow | Key Nextflow concepts and building a pipeline from existing scripts | Intermediate | NextFlow workshop session 2: Key NextFlow concepts | https://github.com/metamaden/NextFlow-Workshop | ||||||||||||||||||||
53 | 2023-12-08 | Nick Eagles | [2023-12-08] Sharing software installations without creating a system-wide module - YouTube | Lmod, conda | Sharing software installations without creating a system-wide module | Intermediate | lmod_sharing_software_rstats | https://twitter.com/LIBDrstats/status/1758621091289768186 | https://bsky.app/profile/libdrstats.bsky.social/post/3klkxhyg6w32u | |||||||||||||||||||
54 | 2023-12-01 | Sean+Nick+Hedia | [2023-12-01] Introduction to Nextflow - YouTube | Nextflow, nf-core | Introduction to Nextflow | Beginner | NextFlow workshop session 1: Introduction to NextFlow | https://github.com/metamaden/NextFlow-Workshop | ||||||||||||||||||||
55 | 2023-11-17 | Joshua Stolz | [2023-11-17] Creating dashboards to navigate omics data - YouTube | Omics Navigator | Creating dashboards to navigate omics data | Beginner | https://github.com/abbvie-external/OmicNavigatorExample/tree/main | |||||||||||||||||||||
56 | 2023-11-10 | CANCELLED due to the 3rd Annual Single Cell Symposium. Register for free at https://www.allcounted.com/s?did=kxn5h0utu5xnf&lang=en_US and see more details at https://twitter.com/LindaOrzolek/status/1697296658785251352 | ||||||||||||||||||||||||||
57 | 2023-11-03 | Cynthia Soto | [2023-11-03] Building pipelines using SLURM dependencies | R and SLURM | Building pipelines using slurm dependencies | Intermediate | https://github.com/cyntsc/Slurm_dependecies | https://github.com/cyntsc/Slurm_dependecies | ||||||||||||||||||||
58 | 2023-10-27 | Nick Eagles | [2023-10-27] Using slurmjobs for interacting with SLURM at JHPCE from R - YouTube | slurmjobs, SLURM | Using slurmjobs for interacting with SLURM at JHPCE from R | Intermediate | https://github.com/LieberInstitute/slurmjobs | https://twitter.com/LIBDrstats/status/1758619151583567940 | https://bsky.app/profile/libdrstats.bsky.social/post/3klkx2ax4fe2k | https://github.com/Nick-Eagles/LIBD_presentations/tree/main/rstats_slurmjobs | ||||||||||||||||||
59 | 2023-10-20 | Geo Pertea | [2023-10-20] R in the back-end - database server alternative to Shiny apps - YouTube | R, PostgreSQL, javascript | R in the back-end - database server alternative to Shiny apps | Advanced | R in the backend not Shiny | |||||||||||||||||||||
60 | 2023-10-13 | CANCELLED due to IDIES2023 that we can register for free at https://www.idies.jhu.edu/news-events/events/idies-annual-symposium/2023-annual-symposium/ | ||||||||||||||||||||||||||
61 | 2023-10-06 | Hedia Tnani | [2023-10-06] Forget about for loops use map instead - YouTube | purrr | Forget about for loops use map instead | Intermediate | https://forgetaboutforloops.netlify.app/ | https://github.com/HediaTnani/Forget_about_for_loops | ||||||||||||||||||||
62 | 2023-09-29 | KJ Benjamin | [2023-09-29] GPU-based eQTL analysis with tensorQTL - YouTube | tensorQTL / python | GPU-based eQTL analysis with tensorQTL | Advanced | rstats: GPU-based eQTL analysis | https://twitter.com/LIBDrstats/status/1707839365387530287 | https://github.com/KrotosBenjamin/eqtl_analysis_tutorial | |||||||||||||||||||
63 | 2023-09-22 | Leonardo Collado Torres | [2023-09-22] ggplot2 themes and building a theme - YouTube | ggplot2, bbplot, ggthemes, ThemePark | ggplot2 themes and building a theme | Intermediate | 2023-09-22 ggplot2 themes and building a theme | https://twitter.com/lcolladotor/status/1705327077535408406 | ||||||||||||||||||||
64 | 2023-09-15 | Leonardo Collado Torres | [2023-09-15] Best git/GitHub practices when adapting code - YouTube | GitHub | Best git/GitHub practices when adapting code | Beginner | 2023-09-15 Best git/GitHub practices when adapting code | https://twitter.com/lcolladotor/status/1704237654873649376 | ||||||||||||||||||||
65 | 2023-09-01 | Cynthia Soto | [2023-09-01] My first job-array in SLURM for R scripts - YouTube | RStudio, R, SLURM | My first job-array in SLURM for R scripts | Beginner | https://docs.google.com/document/d/1iP3BKJ9AudPY8Tu0XQI9ooy87E9t7dT62gSwIXcF3SY/edit?usp=sharing | NA | First Slurm to process cellranger-arc datasets | |||||||||||||||||||
66 | 2023-08-25 | Louise Huuki-Myers | [2023-08-25] BioC2023 recap - YouTube | BioC2023 Recap | Beginner | BioC2023 Recap | ||||||||||||||||||||||
67 | 2023-07-21 | Renee, Daianna, Nick | NA | BioC2023 practice for their long (1.5 hr) SPEAQeasy + smokingMouse workshop | NA | NA | ||||||||||||||||||||||
68 | 2023-07-07 | Hédia Tnani | NA | BioC2023 practice for 45 min qsvaR workshop (presentation + R code part) | NA | NA | ||||||||||||||||||||||
69 | 2023-06-30 | Cynthia Soto | [2023-06-30] R data manipulation and functions - YouTube | RStudio, R | R data manipulation and functions | Beginner | https://speakerdeck.com/cyntsc/r-for-begginers-session2-jun30-2023 | |||||||||||||||||||||
70 | 2023-06-23 | Leonardo Collado Torres | [2023-06-23] Making a documentation website book with bookdown and GitHub actions - YouTube | bookdown, biocthis | Making a documentation website book with bookdown and GitHub actions | Advanced | 2023-06-23 Making a documentation website book with bookdown and GitHub actions | https://twitter.com/lcolladotor/status/1681020937494466560 | ||||||||||||||||||||
71 | 2023-06-09 | Renee + Daianna + Nick + Leo | [2023-06-09] Live debugging a R/Bioconductor package with a docker image - YouTube | biocthis, usethis | Live debugging a R/Bioconductor package with a docker image | Advanced | https://github.com/LieberInstitute/SPEAQeasyWorkshop2023 | https://twitter.com/lcolladotor/status/1681022301587017728 | ||||||||||||||||||||
72 | 2023-06-02 | Cynthia Soto | [2023-06-02] R and RStudio for beginners from zero - YouTube | RStudio, R | R and RStudio for beginners from zero | Beginner | https://speakerdeck.com/cyntsc/r-for-beginners-from-zero | |||||||||||||||||||||
73 | 2023-05-19 | Nick Eagles | [2023-05-19] Building lmod modules at JHPCE - YouTube | Lmod, lua, bash | Building lmod modules at JHPCE | Intermediate | lmod_sharing_software_rstats | https://twitter.com/LIBDrstats/status/1681026158757040128 | ||||||||||||||||||||
74 | 2023-05-12 | Louise Huuki-Myers | [2023-05-12] spatialLIBD: accessing data, visium data visualization, and marker finding - YouTube | spatialLIBD | spatialLIBD: accessing data, visium data visualization, and marker finding | Beginner | https://gist.github.com/lahuuki/c458921794d5dd27029c6238501c2768 | |||||||||||||||||||||
75 | 2023-05-05 | Louise Huuki-Myers, Leonardo Collado Torres | NA | NA | Practice our Genomics for Brain Disorders 2023 material (Leo has a 10 min + 5 QA talk, Louise has a 1 min talk + poster) + Mina Ryten talks | NA | NA | NA | ||||||||||||||||||||
76 | 2023-04-28 | Louise Huuki-Myers | [2023-04-28] Spatial registration with spatialLIBD - YouTube | spatialLIBD | Spatial registration with spatialLIBD | Intermediate | https://research.libd.org/spatialLIBD/articles/guide_to_spatial_registration.html | |||||||||||||||||||||
77 | 2023-04-21 | KJ Benjamin | [2023-04-21] Pretty Posters with LaTeX - YouTube | LaTeX, overleaf | Pretty Posters with LaTeX | Advanced | posters_with_latex | https://twitter.com/LIBDrstats/status/1681025001842155520 | ||||||||||||||||||||
78 | 2023-04-07 | Hedia Tnani | [2023-04-07] Regular Expressions in R - YouTube | Biostrings, rentrez | Regular Expressions in R | Intermediate | https://github.com/HediaTnani/Regular_Expression_R | |||||||||||||||||||||
79 | 2023-03-31 | Geo Pertea | [2023-03-31] Power Ranges: Efficient genome annotation handling in R - YouTube | GenomicRanges, GenomicFeatures, rtracklayer, Rsamtools, SummarizedExperiment, qs | Power Ranges: Efficient genome annotation handling in R | Advanced | https://github.com/gpertea/PowerRangesR | https://twitter.com/LIBDrstats/status/1681023981959401472 | ||||||||||||||||||||
80 | 2023-03-24 | Louise Huuki-Myers | [2023-03-24] Deconvolution with Bisque - YouTube | BisqueRNA, DeconvoBuddies, tidyverse, SingleCellExperiment | Deconvolution with Bisque | Beginner | https://docs.google.com/document/d/ /edit?usp=sharing | |||||||||||||||||||||
81 | 2023-03-17 | Hedia Tnani | [2023-03-17] Intermediate APIs in R: Openai use case - YouTube | httr, jsonlite, tidyverse, xml2, httr2, askpass | Intermediate APIs in R: Openai use case | Advanced | https://github.com/HediaTnani/Int_API_R | |||||||||||||||||||||
82 | 2023-03-10 | Leonardo Collado Torres | [2023-03-10] Updating your Bioconductor packages: devel Git branch and biocthis updates - YouTube | Bioconductor, biocthis, Git, GitHub | Updating your Bioconductor packages: devel Git branch and biocthis updates | Intermediate | 2023-03-10 Updating your Bioconductor packages: devel Git branch and biocthis updates | https://twitter.com/lcolladotor/status/1681019609150005249 | ||||||||||||||||||||
83 | 2023-03-03 | Leonardo Collado Torres | [2023-03-03] Making an R/Bioconductor workshop package for BioC's annual conference - YouTube | usethis, biocthis | Making an R/Bioconductor workshop package for BioC's annual conference | Intermediate | 2023-03-03 Making an R/Bioconductor workshop package for BioC's annual conference | https://twitter.com/lcolladotor/status/1681018703289417728 | ||||||||||||||||||||
84 | 2023-02-24 | Hedia Tnani | [2023-02-24] Getting started with APIs in R - YouTube | httr, jsonlite, tidyverse,xml2 | Getting started with APIs in R | Intermediate | https://github.com/HediaTnani/API_R/blob/main/API_R.qmd | |||||||||||||||||||||
85 | 2023-02-17 | Leonardo Collado Torres | [2023-02-17] Making a R/Bioconductor package for ExperimentHub - YouTube | usethis, biocthis, HubPub, AnnotationHubData | Making a R/Bioconductor package for ExperimentHub | Intermediate | 2023-02-17 Making a R/Bioconductor package for ExperimentHub | https://twitter.com/lcolladotor/status/1681001144330637312 | ||||||||||||||||||||
86 | 2022-12-01 | Leonardo Collado Torres | [2022-12-01] Gene expression heatmaps: benefits of centering and scaling - YouTube | iSEE | Gene expression heatmaps: benefits of centering and scaling | Beginner | https://libd.shinyapps.io/spatialDLPFC_Visium_Sp16_pseudobulk/ | https://twitter.com/lcolladotor/status/1598456517216595968 | https://github.com/LieberInstitute/spatialDLPFC/blob/8467bef2fd47c7df9dbe18cfc67a84261d434adc/code/iSEE_apps_pseudobulk/k09/initial.R#L91-L93 | |||||||||||||||||||
87 | 2022-11-18 | Mine Çetinkaya-Rundel (recording from BioC2022) | BioC 2022 - Hello, Quarto! - YouTube | Quarto, RStudio, rmarkdown | "Hello Quarto!" | Beginner | https://mine.quarto.pub/hello-quarto-bioc/#/hello-quarto-title | https://twitter.com/LIBDrstats/status/1593609792731365376 | ||||||||||||||||||||
88 | 2022-10-21 | Nick Eagles | [2022-10-21] Decision tress with python - YouTube | python, scikit-learn | Decision trees for classification in python | Intermediate | rstats_decision_tree.ipynb | https://twitter.com/LIBDrstats/status/1587544485092737024 | ||||||||||||||||||||
89 | 2022-10-14 | Geo Pertea | [2022-10-14] Compressed and storage-backed matrix data with SummarizedExperiment - YouTube | HDF5Array, Matrix, SummarizedExperiment | Compressed and storage-backed matrix data with SummarizedExperiment | Intermediate | Compressed and storage-backed matrix data with SummarizedExperiment | https://twitter.com/LIBDrstats/status/1587543200369061888 | https://github.com/gpertea/r_delarray | |||||||||||||||||||
90 | 2022-10-07 | Jenny Bryan (recording from RStudio Conf 2020) | https://www.rstudio.com/resources/rstudioconf-2020/object-of-type-closure-is-not-subsettable/ | R error messages, debugging, and more | Object of type ‘closure’ is not subsettable | Beginner | NA | NA | ||||||||||||||||||||
91 | 2022-09-30 | Leonardo Collado Torres | [2022-09-30] How to move files around on JHPCE and setup permissions on /dcs04 - YouTube | getent, rsync, chgrp, nfs4_getfacl, nfs4_setfacl | How to move files around on JHPCE and setup permissions on /dcs04 | Intermediate | https://lcolladotor.github.io/bioc_team_ds/organizing-your-work.html#.YzZOBOzMKX0 | https://twitter.com/lcolladotor/status/1578422331881291783 | ||||||||||||||||||||
92 | 2022-09-23 | Louise Huuki-Myers | [2022-09-23] BioC2022 summary - YouTube | Lots of Bioconductor or soon to be Bioconductor packages! | BioC2022 summary | Beginner | BioC2022 Recap | |||||||||||||||||||||
93 | 2022-09-16 | Nick Eagles, Uma Kaipa | [2022-09-16] pyhere, reprexpy, session_info - YouTube | reprexpy, session_info, pyhere | Explore the reprexpy python package (port of the R reprex package). Touch on other python analogues to R packages, such as session_info and pyhere. | Beginner | NA | https://twitter.com/LIBDrstats/status/1571929716399165440 | https://github.com/Nick-Eagles/LIBD_presentations/blob/main/rstats_pyhere/get_mito_genes.py | |||||||||||||||||||
94 | 2022-09-02 | Leonardo Collado Torres | https://youtu.be/IaclszgZb-g | scran | Finding and interpreting marker genes in sc/snRNA-seq data | Advanced | 2022-09-02 Finding sc/snRNA-seq marker genes | https://twitter.com/lcolladotor/status/1571927812835250177 | ||||||||||||||||||||
95 | 2022-07-08 | Daianna González | NA | NA | Mid-internship presentation | NA | NA | NA | ||||||||||||||||||||
96 | 2022-06-24 | Nick Eagles | [2022-06-24] Introduction to AnnData for SummarizedExperiment users - YouTube | AnnData (python), zellkonverter, SpatialExperiment | Introduction to AnnData for SummarizedExperiment users | Intermediate | rstats_anndata | https://twitter.com/LIBDrstats/status/1540403290000736256 | https://github.com/Nick-Eagles/LIBD_presentations/tree/main/rstats_anndata | |||||||||||||||||||
97 | 2022-06-17 | Josh Stolz | [2022-06-17] Using patchwork to create multipanel figures | patchwork | Using patchwork to create multipanel figures | Beginner | NA | https://twitter.com/JoshStolz2/status/1540315799348314112 | ||||||||||||||||||||
98 | 2022-06-03 | Arthur Feltrin | [2022-06-03] How to use STRINGdb and igraph to run protein-protein interaction network enrichment - YouTube | R, igraph | How to use STRINGdb and igraph to run protein-protein interaction network enrichment | Intermediate | ||||||||||||||||||||||
99 | 2022-05-27 | Louise Huuki-Myers | [2022-05-27] How to find candidate TREGs in snRNA-seq, including filtering & Rank Invariance steps - YouTube | TREG | How to find candidate TREGs in snRNA-seq data, including filtering and Rank Invariance steps | Intermediate | rstats | |||||||||||||||||||||
100 | 2022-05-20 | Leonardo Collado Torres | [2022-05-20] How to make your personal website with R - YouTube | git, github, usethis, postcards, fontawesome, gitcreds | How to make your personal website with R | Beginner | 2022-05-20 How to make your personal website with R | https://twitter.com/lcolladotor/status/1539689473121759233 |