14 Mar 2025
New blog post: Initial impressions from testing Posit Connect
lcolladotor.github.io/2025/0…
I describe our use case and why I think that Posit Connect will be helpful for our @lieberinstitute work moving forward
@posit_pbc #RStats #shiny #shinyapps #spatialLIBD #iSEE @LIBDrstats
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12 Jun 2024
I'm excited to present tomorrow about #spatialLIBD & analysis of spatially-resolved transcriptomics #Visium data with #rstats & @Bioconductor tools
Thanks for inviting me @FLGenomics!
Check 👀 the slides here 👇🏽
speakerdeck.com/lcolladotor/…
@LieberInstitute @jhubiostat @10xGenomics
12 Apr 2024
Join us in welcoming @LColladoTor (Investigator, @LieberInstitute, Assistant Professor, Department of Biostatistics, @JohnsHopkinsSPH) to #FOGBoston, where he’ll be involved in our #spatial data analysis workshop. Register now: hubs.la/Q02r3vL00
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25 May 2024
Sure, check research.libd.org/spatialDLP…. Available via Globus and the @NIMHgov Data Archive (NDA)
Processed data for both projects is also available through #spatialLIBD::fetch_data()
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23 May 2024
4) We’ve shared this data with the scientific community through interactive web tools and our R package #spatialLIBD @Bioconductor #OpenScience #OpenData
🔗research.libd.org/spatialDLP…
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15 May 2024
Check out the updates to #spatialLIBD that Nick-Eagles (@github) introduced to the latest version available from @Bioconductor 3.19 release
Visualize multiple genes with the #spatialLIBD::vis_gene() family of functions
research.libd.org/spatialLIB…
#rstats
youtu.be/_dBPZ62t40c
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16 Apr 2024
If you haven't registered for #FoGBoston you can do so for free at hubs.la/Q01MkQpf0
See you soon in Boston, MA, USA!
#spatialLIBD #Visium #spatialomics
12 Apr 2024
Join us in welcoming @LColladoTor (Investigator, @LieberInstitute, Assistant Professor, Department of Biostatistics, @JohnsHopkinsSPH) to #FOGBoston, where he’ll be involved in our #spatial data analysis workshop. Register now: hubs.la/Q02r3vL00
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spatialLIBD
an R/Bioconductor package to visualize spatially-resolved transcriptomics data
SpatialExperiment
Interactively visualizing #10xVisium #SpatialTranscriptomics
bioconductor.org/packages/re…
@lcolladotor BMC Genomics 2022 @LieberInstitute
bmcgenomics.biomedcentral.co…
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15 Nov 2023
¡Felicidades Keri @martinowk!
The #spatialLIBD team has benefited a lot from your ideas, orchestration, insights, leadership, and support!
Also many at @LieberInstitute have benefited from your role as Head of Education & Training Programs
Thanks again Keri! Kudos to you!! 👏🏽
14 Nov 2023
See the award acceptance from Dr. Martinowich (@martinowk) here: youtube.com/watch?v=wcRPRJvd…
Video from her nominator, Dr. Daniel Weinberger: youtube.com/watch?v=V9v0E7S9…
More info about Dr. Martinowich and her pioneering work can be seen here: files.constantcontact.com/61…
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27 Oct 2023
Hehehe
See how I used the #paletteer 📦 in #spatialLIBD. I got tired of people asking for plots with X or Y color :P
github.com/LieberInstitute/s… to 129 & elsewhere
For more:
github.com/EmilHvitfeldt/pal…
&
emilhvitfeldt.github.io/r-co…
By @Emil_Hvitfeldt are great 🤩
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12 Oct 2023
Major update of DESpace pre-print.
In all our benchmarks, further to SVG tools, we added comparisons to marker gene methods, and to SpatialLIBD wrappers.
biorxiv.org/content/10.1101/…
19 Apr 2023
DESpace: a new method to discover spatially variable genes (SVGs).
DESpace is on Bioconductor: bioconductor.org/packages/DE…
Here is a pre-print: doi.org/10.1101/2023.04.17.5…
Work from Peiying Cai, @markrobinsonca and myself.
A short thread. 1/5
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5 Sep 2023
My #rstats stickers stash is starting to run low. I last printed stickers around March 2020
Maybe it’s time to print some more @RLadiesBmore @CDSBMexico ones. Hmm… #spatialLIBD & other ones from our packages 📦
What else? Are there any @stickermule discounts for #rstats?
1 Sep 2023
Ya están las etiquetas de @CDSBMexico y @RLadiesBmore en el auditorio del @ccg_unam
#LCG20 @lcgunam @lcgejunam
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4 Aug 2023
I liked how #tidyomics is compatible with #plotly.
Looks like I’ll be able to avoid some more complicated code at #spatialLIBD. Like lines 608 to 633 at github.com/LieberInstitute/s… where I want to use highlight_key()
@steman_research @mikelove
#BioC2023
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3 Aug 2023
But actually come checkout my #spatialDLPFC poster this afternoon for even more #spatialLIBD content 😁 #BioC2023
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2 Aug 2023
Lots of brain slides at the #BioC2023 spatial session 👀🧠 Join @lcolladotor and I at 2pm for our #spatialLIBD workshop to learn to access this ✨all-star dataset✨ and about our spatial transciptomics tools!
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1 Aug 2023
I also got the opportunity to work with really cool @Bioconductor packages such as #BayesSpace and #spatialLIBD to perform layer registration of gene unsupervised clusters to known-layer-marker-gene expression.
ALT Supplementary Figure 11. Unsupervised clustering with BayesSpace separates white and gray matter clusters in all tissue sections.
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21 Jul 2023
Looking forward to #BioC2023 !
@lcolladotor and I will be demoing the #spatialLIBD package 💻🔧 and I will be presenting new data and findings in my poster on #spatialDLPFC 🧠🧬 from our preprint 👩🔬
🔗doi.org/10.1101/2023.02.15.5…
21 Jul 2023
**Speaker Spotlight**
Louise Huuki-Myers
Website: buff.ly/44gTkCz
Twitter: @lahuuki
Her #BioC2023 talk will be on Analyzing Spatially-Resolved Transcriptomics Data from Visium using spatialLIBD
Registration for BioC2023: buff.ly/3nKEq72
ALT Staff Scientist at the Lieber Institute for Brain Development. Will be presenting work in spatially resolved transcriptomics in a Package Demo for #spatialLIBD and a poster on #SpatialDLPFC.
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21 Jul 2023
**Speaker Spotlight**
Louise Huuki-Myers
Website: buff.ly/44gTkCz
Twitter: @lahuuki
Her #BioC2023 talk will be on Analyzing Spatially-Resolved Transcriptomics Data from Visium using spatialLIBD
Registration for BioC2023: buff.ly/3nKEq72
ALT Staff Scientist at the Lieber Institute for Brain Development. Will be presenting work in spatially resolved transcriptomics in a Package Demo for #spatialLIBD and a poster on #SpatialDLPFC.
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10 Jul 2023
It's an adaptation/extension from lcolladotor.github.io/rnaseq… github.com/lcolladotor/rnase… which is in Spanish 🇲🇽 @lcgunam
Packages 📦 highlighted: #SummarizedExperiment #iSEE #smokingMouse #biocthis #recount3 #ExploreModelMatrix #limma #variancePartition #ComplexHeatmap #spatialLIBD
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25 May 2023
Thank you #GBD23 @MinaRyten @LabGandhi John Hardy 🇬🇧 for hosting us!🙌🏽
Hopefully our #deconvochallenge #spatialLIBD #spatialDLPFC #Visium_SPG_AD work @Bioconductor 📦s @10xGenomics @LieberInstitute data will be useful to you
@eventsWCS @UCLchildhealth @TheCrick @UCLIoN @ucl
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25 May 2023
Keep an eye on #spatialLIBD - a bioconductor package and shiny web application for #spatialtranscriptomics analysis (presented yesterday by @lahuuki @lcolladotor @LieberInstitute research.libd.org/spatialLIB… ) @UCLchildhealth
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