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LIBD rstats club
http://research.libd.org/rstatsclub/#.XpB1SNNKiL8
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Code of conduct
Twitterhttps://twitter.com/LIBDrstats
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Announcements and reminders
https://groups.google.com/d/forum/libd-rstats-club
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Suggest topicshttps://forms.gle/mREfqxbaikh7FAhf6
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DatePresenterRecording LinkSoftware / R packagesTopicDifficulty level: beginner, intermediate, advancedSlides / materialTwitter / bskyCodeNotes by you
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TBDLouise Huuki-MyersdeconvoBuddiesHow to use deconvoBuddies for deconvolution of bulk RNA-seq dataIntermediate
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TBDDavid Zhangpoetry, cookiecutterDeveloping python packages; an R users perspectiveAdvancedhttps://py-pkgs.org/
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TBDGeo PertearwrapExplore rwrap and rpy2 from https://twitter.com/kpj_py/status/1485650880187805698?s=21Intermediate
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TBDLeonardo Collado TorresUsing git-status-size and demonstration of how to use git add on active projectsBeginner
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TBDLeonardo Collado TorresWriting blog postsBeginner
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TBDLeonardo Collado TorresRStudio projects and shortcutsBeginner
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TBDGeo Perteaqs, fstqs: faster save/load of R objects;
fst: fast dataframe save/load, with slice loading option		Beginner
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TBDGeo Perteaconda, python, Rsetting up isolated conda enviroments Advanced
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TBDHedia TnaniSQL, R, & dplyrIntermediate
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TBDHedia TnaniHow to make an R package from an RmarkdownAdvancedHow to make an R package from an Rmarkdown
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TBDHedia Tnani + Geo Pertealimma, edgeR, tximportTranscript level differential expression - using the latest practicesIntermediate
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TBDCynthia SotoSeurat, SignacMultiOmics with Seurat + SignacBeginner
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2024-02-23
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2024-02-16
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2024-02-09
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2024-02-02
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2024-01-26
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2024-01-19(Leo ✈️)
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2024-01-12
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2024-01-05
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2023-12-29CANCELLED (Winter Holiday)
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2023-12-22
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2023-12-15
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2023-12-08Sean+Nick+Hedia
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2023-12-01Sean+Nick+HediaNextflow, nf-coreIntroduction to nextflowBeginnerNextFlow workshop session 1: Introduction to NextFlowhttps://github.com/metamaden/NextFlow-Workshop
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2023-11-24CANCELLED (Thanksgiving)
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2023-11-17Joshua StolzOmics NavigatorCreating dashboards to navigate omics dataBeginner
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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
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2023-11-03Cynthia SotoR and SLURMBuilding pipelines using slurm dependenciesIntermediatehttps://github.com/cyntsc/Slurm_dependecieshttps://github.com/cyntsc/Slurm_dependecies
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2023-10-27Nick Eaglesslurmjobs, SLURMUsing slurmjobs for interacting with SLURM at JHPCE from RIntermediatehttps://github.com/Nick-Eagles/LIBD_presentations/tree/main/rstats_slurmjobs
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2023-10-20Geo Perteahttps://youtu.be/0sAsMQZoBMcR, PostgreSQL, javascriptR in the back-end - database server alternative to Shiny appsAdvancedR in the backend not Shiny
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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/
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2023-10-06Hedia Tnanihttps://youtu.be/dGu2IoAFh3cpurrrForget about for loops use map insteadIntermediatehttps://forgetaboutforloops.netlify.app/https://github.com/HediaTnani/Forget_about_for_loops
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2023-09-29KJ Benjaminhttps://youtu.be/R9yM0q5wVaItensorQTL / pythonGPU-based eQTL analysis with tensorQTLAdvancedrstats: GPU-based eQTL analysishttps://twitter.com/LIBDrstats/status/1707839365387530287https://github.com/KrotosBenjamin/eqtl_analysis_tutorial
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2023-09-22Leonardo Collado Torreshttps://youtu.be/7GqXssfzQYEggplot2, bbplot, ggthemes, ThemeParkggplot2 themes and building a themeIntermediate2023-09-22 ggplot2 themes and building a themehttps://twitter.com/lcolladotor/status/1705327077535408406
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2023-09-15Leonardo Collado Torreshttps://youtu.be/Lzl1zu-HCZ4GitHubBest git/GitHub practices when adapting codeBeginner2023-09-15 Best git/GitHub practices when adapting codehttps://twitter.com/lcolladotor/status/1704237654873649376
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2023-09-01Cynthia Sotohttps://youtu.be/kkOIcIFS5jgRStudio, R, SLURMMy first job-array in SLURM for R scriptsBeginnerhttps://docs.google.com/document/d/1iP3BKJ9AudPY8Tu0XQI9ooy87E9t7dT62gSwIXcF3SY/edit?usp=sharing NAFirst Slurm to process cellranger-arc datasets
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2023-08-25Louise Huuki-Myershttps://youtu.be/C9ejtqOa5zoBioC2023 RecapBeginnerBioC2023 Recap
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2023-07-21Renee, Daianna, NickNABioC2023 practice for their long (1.5 hr) SPEAQeasy + smokingMouse workshopNANA
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2023-07-07Hédia TnaniNABioC2023 practice for 45 min qsvaR workshop (presentation + R code part)NANA
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2023-06-30Cynthia Sotohttps://youtu.be/c7kJO6K4Y4URStudio, RR data manipulation and functionsBeginnerhttps://speakerdeck.com/cyntsc/r-for-begginers-session2-jun30-2023
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2023-06-23Leonardo Collado Torreshttps://youtu.be/-luX8CpXzbAbookdown, biocthisMaking a documentation website book with bookdown and GitHub actionsAdvancedhttps://docs.google.com/document/d/1nXhkUxN5ViMcRM3ERXj8muHFSvJE6xrjiZ97XwUuVoo/edit?usp=sharinghttps://twitter.com/lcolladotor/status/1681020937494466560
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2023-06-09Renee + Daianna + Nick + Leohttps://youtu.be/SWS4Hs6jTMwbiocthis, usethisLive debugging a R/Bioconductor package with a docker imageAdvancedhttps://github.com/LieberInstitute/SPEAQeasyWorkshop2023https://twitter.com/lcolladotor/status/1681022301587017728
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2023-06-02Cynthia Sotohttps://youtu.be/T51DRWeuKm8RStudio, RR and RStudio for beginners from zeroBeginnerhttps://speakerdeck.com/cyntsc/r-for-beginners-from-zero
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2023-05-19Nick Eagleshttps://youtu.be/8w6JDsrgqVsLmod, lua, bashBuilding lmod modules at JHPCEIntermediatehttps://docs.google.com/presentation/d/1v4Pnhy_ycd7oi0jRe_LU_0B1tQrbXFUxSIuJTGI1FPI/edit?usp=sharinghttps://twitter.com/LIBDrstats/status/1681026158757040128
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2023-05-12Louise Huuki-Myershttps://youtu.be/6aG5X20dZvMspatialLIBDspatialLIBD: accessing data, visium data visualization, and marker finding Beginnerhttps://gist.github.com/lahuuki/c458921794d5dd27029c6238501c2768
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2023-05-05Louise Huuki-Myers, Leonardo Collado TorresNANAPractice our Genomics for Brain Disorders 2023 material (Leo has a 10 min + 5 QA talk, Louise has a 1 min talk + poster) + Mina Ryten talksNANANA
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2023-04-28Louise Huuki-Myershttps://youtu.be/TW-MUz9Mhh8spatialLIBDSpatial registration with spatialLIBDIntermediatehttps://research.libd.org/spatialLIBD/articles/guide_to_spatial_registration.html
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2023-04-21KJ Benjaminhttps://youtu.be/3fARngcfXLcLaTeX, overleafPretty Posters with LaTeXAdvancedhttps://docs.google.com/document/d/17e-BkWGnINd07A9dIWNSOvbhq5ccdFPnWOyGWtb0iNk/edit?usp=sharinghttps://twitter.com/LIBDrstats/status/1681025001842155520
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2023-04-07Hedia Tnanihttps://youtu.be/xa6gtPDP8TIBiostrings, rentrezRegular Expressions in R Intermediatehttps://github.com/HediaTnani/Regular_Expression_R
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2023-03-31Geo Perteahttps://youtu.be/FEnc2l3FuUYGenomicRanges, GenomicFeatures, rtracklayer, Rsamtools, SummarizedExperiment, qsPower Ranges: Efficient genome annotation handling in RAdvancedhttps://github.com/gpertea/PowerRangesRhttps://twitter.com/LIBDrstats/status/1681023981959401472
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2023-03-24Louise Huuki-Myershttps://youtu.be/Nx_W8KJ6dwoBisqueRNA, DeconvoBuddies, tidyverse, SingleCellExperimentDeconvolution with BisqueBeginnerhttps://docs.google.com/document/d/ /edit?usp=sharing
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2023-03-17Hedia Tnanihttps://youtu.be/sxlBMBFNLCkhttr, jsonlite, tidyverse, xml2, httr2, askpassIntermediate APIs in R: Openai use caseAdvancedhttps://github.com/HediaTnani/Int_API_R
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2023-03-10Leonardo Collado Torreshttps://youtu.be/Rbadjup630wBioconductor, biocthis, Git, GitHubUpdating your Bioconductor packages: devel Git branch and biocthis updatesIntermediatehttps://docs.google.com/document/d/117p0sKFKpMSZy90ZWc56_J-MhwfSMEnMVkqAVqZStaA/edit?usp=sharinghttps://twitter.com/lcolladotor/status/1681019609150005249
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2023-03-03Leonardo Collado Torreshttps://youtu.be/Ewa89GMTgPUusethis, biocthisMaking an R/Bioconductor workshop package for BioC's annual conferenceIntermediatehttps://docs.google.com/document/d/1FOgRmu7a3KU9FEzT3mQ4KNrqqS7RhOL-lLJWj_6BIeE/edit?usp=sharinghttps://twitter.com/lcolladotor/status/1681018703289417728
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2023-02-24Hedia Tnanihttps://youtu.be/YJ_cQEt3USkhttr, jsonlite, tidyverse,xml2Getting started with APIs in RIntermediatehttps://github.com/HediaTnani/API_R/blob/main/API_R.qmd
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2023-02-17Leonardo Collado Torreshttps://youtu.be/e42DkvRYescusethis, biocthis, HubPub, AnnotationHubDataMaking a R/Bioconductor package for ExperimentHubIntermediatehttps://docs.google.com/document/d/1WT9iRW6iQMVCDWd4KnpAO8Qvk2GREZ4RtNBJ92FxaWo/edit?usp=sharinghttps://twitter.com/lcolladotor/status/1681001144330637312
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2022-12-01Leonardo Collado Torreshttps://youtu.be/c8ffeFVUzk8iSEEGene expression heatmaps: benefits of centering and scalingBeginnerhttps://libd.shinyapps.io/spatialDLPFC_Visium_Sp16_pseudobulk/https://twitter.com/lcolladotor/status/1598456517216595968https://github.com/LieberInstitute/spatialDLPFC/blob/8467bef2fd47c7df9dbe18cfc67a84261d434adc/code/iSEE_apps_pseudobulk/k09/initial.R#L91-L93
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2022-11-18Mine Çetinkaya-Rundel (recording from BioC2022)https://youtu.be/YVa5cdkypbwQuarto, RStudio, rmarkdown"Hello Quarto!"Beginnerhttps://mine.quarto.pub/hello-quarto-bioc/#/hello-quarto-titlehttps://twitter.com/LIBDrstats/status/1593609792731365376
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2022-10-21Nick Eagleshttps://youtu.be/-qFz7PwWEeYpython, scikit-learnDecision trees for classification in pythonIntermediatehttps://colab.research.google.com/drive/1rSto3CR_Iaj-M6tEWLU0i12F2IbXR6n0?usp=sharinghttps://twitter.com/LIBDrstats/status/1587544485092737024
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2022-10-14Geo Perteahttps://youtu.be/YoBW7IiNzQAHDF5Array, Matrix, SummarizedExperimentCompressed and storage-backed matrix data with SummarizedExperiment Intermediatehttps://docs.google.com/presentation/d/1vWcrRAkxjLDfhvJZ0QXy0ekYiq6cAAlzNYl-TSEaiWI/edit?usp=sharinghttps://twitter.com/LIBDrstats/status/1587543200369061888https://github.com/gpertea/r_delarray
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2022-10-07Jenny 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 moreObject of type ‘closure’ is not subsettableBeginnerNANA
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2022-09-30Leonardo Collado Torreshttps://youtu.be/Y7fFLX3fw9Agetent, rsync, chgrp, nfs4_getfacl, nfs4_setfaclHow to move files around on JHPCE and setup permissions on /dcs04Intermediatehttps://lcolladotor.github.io/bioc_team_ds/organizing-your-work.html#.YzZOBOzMKX0https://twitter.com/lcolladotor/status/1578422331881291783
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2022-09-23Louise Huuki-Myershttps://youtu.be/XxLnc0C-L4wLots of Bioconductor or soon to be Bioconductor packages!BioC2022 summaryBeginnerhttps://docs.google.com/presentation/d/1Ds7AYZX6JjKI3Du_mXVJFdYyJgOX4Oplu2ofahHliSI/edit?usp=sharing
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2022-09-16Nick Eagles, Uma Kaipahttps://youtu.be/-GdqCf0dFPUreprexpy, session_info, pyhereExplore the reprexpy python package (port of the R reprex package). Touch on other python analogues to R packages, such as session_info and pyhere.BeginnerNAhttps://twitter.com/LIBDrstats/status/1571929716399165440https://github.com/Nick-Eagles/LIBD_presentations/blob/main/rstats_pyhere/get_mito_genes.py
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2022-09-02Leonardo Collado Torreshttps://youtu.be/IaclszgZb-gscranFinding and interpreting marker genes in sc/snRNA-seq dataAdvancedhttps://docs.google.com/document/d/1BeMtKgE7gpmNywInndVC9o_ufopn-U2EZHB32bO7ObM/edit?usp=sharinghttps://twitter.com/lcolladotor/status/1571927812835250177
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2022-07-08Daianna GonzálezNANAMid-internship presentationNANANA
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2022-06-24Nick Eagleshttps://youtu.be/eNUSreI77aAAnnData (python), zellkonverter, SpatialExperimentIntroduction to AnnData for SummarizedExperiment usersIntermediatehttps://docs.google.com/presentation/d/1V4N7xnRSGKkgo7ySnwjmqaW8S9ABCjb8zu9g3aWQ0Ak/edit?usp=sharinghttps://twitter.com/LIBDrstats/status/1540403290000736256https://github.com/Nick-Eagles/LIBD_presentations/tree/main/rstats_anndata
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2022-06-17Josh Stolzhttps://youtu.be/-aQRghyRSaUpatchworkUsing patchwork to create multipanel figuresBeginnerNAhttps://twitter.com/JoshStolz2/status/1540315799348314112
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2022-06-03Arthur Feltrinhttps://youtu.be/JEaNhUq_8rAR, igraphHow to use STRINGdb and igraph to run protein-protein interaction network enrichmentIntermediate
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2022-05-27Louise Huuki-Myershttps://youtu.be/2Q3Ye6yoAeATREGHow to find candidate TREGs in snRNA-seq data, including filtering and Rank Invariance stepsIntermediatehttps://docs.google.com/document/d/1ef2OZW0C08crrbR4sK-8Qbyg6cug6P7x3-F6HTN-WEA/edit?usp=sharing
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2022-05-20Leonardo Collado Torreshttps://youtu.be/9LUCZAx3SlUgit, github, usethis, postcards, fontawesome, gitcredsHow to make your personal website with RBeginnerhttps://docs.google.com/document/d/1K7q1mBoEJCwJe-PIGarZZ7-aBx1aMravqD7KRnvyIMU/edit?usp=sharinghttps://twitter.com/lcolladotor/status/1539689473121759233
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2022-05-04Leonardo Collado Torreshttps://youtu.be/XD4imW80qWwgit, GitHubBioconductor: git commands for package maintainersIntermediatehttp://bioconductor.org/developers/how-to/git/sync-existing-repositories/ and http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/, both from http://bioconductor.org/developers/how-to/git/. We also used http://bioconductor.org/developers/rss-feeds/, https://ifttt.com/login, and https://www.git-tower.com/learn/git/faq/delete-local-branch.https://twitter.com/lcolladotor/status/1522560935797432321
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2022-04-29Nick Eagleshttps://youtu.be/pI8-myU8ZDsBiocMAPOverview of BiocMAP for processing WGBS dataBeginnerhttps://docs.google.com/presentation/d/1a5D_3emoXyka2EUkBtGJgoXt4wWz5J3HA8jh6hA7pds/edit?usp=sharinghttps://twitter.com/LIBDrstats/status/1520087573300871168
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2022-04-22Josh Stolz, Abby SpanglerNAVariantAnnotationHow to annotate a VCFBeginnerhttps://github.com/abspangler13/VariantAnnotationNA
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2022-04-15Madhavi TippaniNAPractice LIBD seminar presentationNANA
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2022-04-08Leonardo Collado Torreshttps://youtu.be/vI2H59hKdQYGitHubGitHub organization features, settings, search & discussionBeginnerhttps://docs.github.com/en/search-githubhttps://twitter.com/LIBDrstats/status/1516591210546089985
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2022-04-01Nick Eagles, Louise Huuki-Myershttps://youtu.be/zOMUXYHtVJMtensorQTLHow to use the GPU queue with tensorQTL as an exampleIntermediatehttps://docs.google.com/presentation/d/1u1cHklp1JHPRjaaDOupbBIo0Ty439I2M-SCetgl3Uxk/edit?usp=sharinghttps://twitter.com/lahuuki/status/1516481218908344322https://gist.github.com/lahuuki/6fa1575bb15d80aeecdcabc5e2ad5f16
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2022-03-18Leonardo Collado Torreshttps://youtu.be/LjWr39C1Z_Qrmote, rmate, TextMateHow to use rmote and rmate on JHPCEIntermediatehttps://docs.google.com/document/d/1vj0xa_qZTIgsnooW_9_j44Low1UbSIufnlGXCgL_YCU/edit?usp=sharinghttps://twitter.com/LIBDrstats/status/1504893191459258369
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2022-03-11Leonardo Collado Torreshttps://youtu.be/luzyACCZkLYpaletteer, colorblindr, Polychrome, colorspace, dittoSeq, viridis, viridisLite, scatterHatchChoosing colors in RBeginnerhttps://docs.google.com/document/d/1o9LkKu8Ns8FioSrfzxOSycO9f8tZK1t79-UwS0cc1bg/edit?usp=sharinghttps://twitter.com/LIBDrstats/status/1502387817044865025
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2022-03-04Leonardo Collado Torreshttps://youtu.be/D6t2GR7xaTEJHPCE, SpatialExperiment, spatialLIBDUsing R/devel at JHPCE and your computer. Useful for accessing the latest versions of Bioconductor packages or when preparing oneAdvancedhttps://docs.google.com/document/d/1DD9MUI2e3jp5S8C3PWRulZ4jwbXo94D3UTCQNJl_-Qo/edit?usp=sharinghttps://twitter.com/LIBDrstats/status/1502384842566029313
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2022-02-25Leonardo Collado Torreshttps://youtu.be/0_DvP3n2yLcsgejobsHow to setup bash loops and nested qsubsIntermediatehttp://research.libd.org/sgejobs/https://twitter.com/LIBDrstats/status/1502383504029478912
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2022-02-11David Zhanghttps://youtu.be/l_-3rhkvJN0ggtranscriptggtranscript: Visualising transcript structure and annotation using ggplot2Intermediatehttps://github.com/dzhang32/ggtranscripthttps://twitter.com/LIBDrstats/status/1502382350155403266
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2022-02-04David Zhanghttps://youtu.be/dJapUTXNwI4https://github.com/lorenzwalthert/precommitPre-commit hooks in RAdvancedhttps://github.com/dzhang32/rstats_preshttps://twitter.com/LIBDrstats/status/1502381597009403906
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2022-01-28Leonardo Collado Torreshttps://youtu.be/-6sZyp0hNwUreprex, JHPCE, GitHubAsking for help for R errors in JHPCEIntermediatehttps://docs.google.com/document/d/14ax6UIlgFGnrZSR1HQ-2vLYhCYLXAGRiib5edMhxLGA/edit?usp=sharinghttps://twitter.com/LIBDrstats/status/1487147235557232642
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2021-12-10Geo Perteahttps://youtu.be/2A_Zm1ej6Gcdata.table, tidyverse/dtplyrReading, writing and manipulating large tables with RBeginnerhttps://github.com/gpertea/R_data_table/blob/main/data_table.Rmdhttps://twitter.com/LIBDrstats/status/1472640732133535745
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2021-12-03Abby Spanglerhttps://youtu.be/AJFN-eSQyKsSpatialExperimentUnderstanding the structure of SpatialExperiment objectsBeginnerhttps://docs.google.com/presentation/d/1bcVIyouI10rgPczeDv8zQ30miSyjN2izUwn17A4nvoM/edit#slide=id.phttps://twitter.com/LIBDrstats/status/1504864645219115008
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2021-11-26THANKSGIVING
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2021-11-19Apuã Paquolahttps://youtu.be/sfQAxfy0JgArfReproducibility FrameworkIntermediatehttps://github.com/apuapaquola/rfhttps://twitter.com/LIBDrstats/status/1504863744324636672
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2021-11-12Josh Stolzhttps://youtu.be/f3F8yTREzKAVariantAnnotationAccessing DNA genotype dataBeginnerhttps://bioconductor.org/packages/VariantAnnotationhttps://twitter.com/JoshStolz2/status/1466107659493408775
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2021-11-05Leonardo Collado Torreshttps://youtu.be/exVvZhg5ggYcareer advice/pathsA field guide to cultivating computational biologyBeginnerhttps://doi.org/10.1371/journal.pbio.3001419https://twitter.com/LIBDrstats/status/1466105202809794563
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2021-10-29Leonardo Collado Torreshttps://youtu.be/13bIatqNHH8BioconductorBioconductor 3.14 release overviewBeginnerhttps://docs.google.com/spreadsheets/d/13MBhBdl8fbHEQPQGrR8qutSGMIzx8bpm0EWXQy3EzlU/edit?usp=sharinghttps://twitter.com/LIBDrstats/status/1466104192682975232
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2021-09-10KJ Benjaminhttps://youtu.be/K-6yhDv1Zdopython, scikit-imageImage Processing in Python, Part 2Intermediatehttps://colab.research.google.com/drive/1fICXIl_JUV5zem_h5Dfm-l5mFBQCNHvj?usp=sharinghttps://twitter.com/LIBDrstats/status/1466103365155233796