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El paper es el siguiente, y os comparto también el link por si queréis leerlo: ⛓️ LINK: arxiv.org/abs/2304.05332

RNA floating in solution is partitioned into single-cell droplets along with cells. This ambient RNA confounds downstream analysis. Tools like SoupX and DecontX attempt to remove this background. Here are lung cells positive (yellow) for one gene before and after SoupX. 🧵(1/2)

What a day! Alba Garrido defended her thesis on international IBD day. So special 💜

(1/n) some thoughts about foundation models for single-cell biology upon publication of an interesting paper (geneformer) today in nature introducing a foundation model trained on 30M cells with cool applications nature.com/articles/s4158…

#AI methods for #denoising of #scRNAseq data have recently raised huge attention Yet, existing approaches lead to dramatically different (dangerous?) data transformations In the most extensive review to date we compare 19 methods and provide guidelines doi.org/10.1093/bib/bb…

In scRNA-seq analysis, "overcorrection" of batch effects is a frequent cause for loss of important biological variability. Using prior celltype knowledge is a powerful way to limit overcorrection and should be more common practice. Sharing new preprint! biorxiv.org/content/10.110…

Desde ACCU España estamos elaborando un estudio sobre el impacto económico, sanitario y social que tienen la enfermedad de Crohn y la colitis ulcerosa, desde la perspectiva de las personas con EII. ¿Nos ayudas rellenando el cuestionario? Enlace: ecrd.outcomes10.com/s3/ACCU-Cuesti…

📢 Just published a breakthrough paper in Nature! 🧪 Our study revealed intriguing insights into IBD, unraveling complexity and patient-to-patient heterogeneity. Kudos to Alba Garrido and our IBD research team! #IBD #NaturePublication 📚🔬 nature.com/articles/s4146…

The pub with the highest altmetric score in our search last week appeared in nature: x.com/ibd_bcn/status… Congrats Alba Garrido Ana Corraliza IBD lab and team 🙌🧵 2/5

On October 23, we will submit Seurat v5 to CRAN, and once accepted it will become the default version for new installs. A few notes on v5 below:

Long-read whole-genome analysis of human single cells | Nature Communications nature.com/articles/s4146…

Un estudi explora les interaccions cel·lulars en la malaltia inflamatòria intestinal Investigadors del Clínic-IDIBAPS publiquen un estudi a Nature Communications que revela els tipus cel·lulars implicats en la variabilitat entre pacients en #MII 👉tuit.cat/416ka

For those interested in reviewing our observations, the slides can be found on our website under "Resources." We welcome constructive feedback and suggestions for analysis. martelottolab.org

Congrats to vicki for her excellent oral communication "Dissecting submucosal fibroblast populations of human colon Crohn's Disease through spatial transriptomics." Best communication award at the 2nd International Workshop on Liver and Gut Fibrosis #FibrosisValencia

Woww!! 10x Genomics Cell Ranger Code is finally public! License enables only "internal use" of the code but still it's a tremendous leap towards transparency. github.com/10XGenomics/ce…

Sceodesic: Navigating the manifold of single-cell gene coexpression to discover interpretable gene programs biorxiv.org/content/10.110…

¡Oficial! Seremos la sede del III Congreso de R y XIV Jornadas de Usuarios de R Comunidad R Hispano Tomamos el relevo desde Barcelona con el compromiso de mantener el nivel y organización que ellos han marcado. Para ello, contaremos con el apoyo del IMUS. ¡Sevilla y R! Nos vemos en ná

Yesterday, my colleague Marc and I had the chance of presenting at the Hispanic R Congress our projects in understanding IBD using single-cell and spatial transcriptomics 🌟 #RqueR Conferencia R España #13JRes

Gracias a todos los asistentes, talleristas, ponentes y comunicadores. A la UPF Barcelona y Comunicació UPF por ofrecer el espacio del II Congreso R y por la ayuda logística, a BSC-CNS como partner organizador y a todos los sponsors Comunidad R Hispano Orange España Nos vemos en Sevilla!

The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In biorxiv.org/content/10.110… w/ Joseph Rich et al. we take a close look. The results are 👀 1/🧵