GitHub - omnideconv/spacedeconv: A unified interface to spatial transcriptomics deconvolution tools github.com/omnideconv/spa…

Unagi: Deep Generative Model for Deciphering Cellular Dynamics and In-Silico Drug Discovery in Complex Diseases researchsquare.com/article/rs-367…

Integrating single-cell RNA and T cell/B cell receptor sequencing with mass cytometry reveals dynamic trajectories of human peripheral immune cells from birth to old age nature.com/articles/s4159…

goloco: a web application to create genome scale information from surprisingly small experiments bmcbioinformatics.biomedcentral.com/articles/10.11…

Scaling up spatial transcriptomics for large-sized tissues: uncovering cellular-level tissue architecture beyond conventional platforms with iSCALE😳 biorxiv.org/content/10.110…

Smoothie: Efficient Inference of Spatial Co-expression Networks from Denoised Spatial Transcriptomics Data biorxiv.org/content/10.110…

Interested in exploring Vevo Therapeutics’s massive Tahoe-100M single-cell perturbation dataset? #Scanpy now supports out-of-core analysis, powered by Dask—allowing you to seamlessly work with a single huge AnnData object without loading everything into memory. 🔗 theislab.github.io/vevo_Tahoe_100…

nf-VueGen: Automating the generation of scientific reports (with Nextflow) biorxiv.org/content/10.110… 🧬🖥️🧪 github.com/Multiomics-Ana…

Decoding aging-dependent regenerative decline across tissues at single-cell resolution hubs.li/Q037YDZy0 Open stem cell research from Cell Stem Cell

COVET: The covariance environment defines cellular niches for spatial inference nature.com/articles/s4158…

Spotiphy (spot imager with pseudo-single-cell-resolution histology), a computational toolkit that transforms sequencing-based spatial transcriptomics data into single-cell-resolved whole-transcriptome images. nature.com/articles/s4159…

Still time to apply! We’re hiring at CHU Sainte-Justine, join our lab! 🐠🩸

Identification and characterization of cell niches in tissue from spatial omics data at single-cell resolution nature.com/articles/s4146…

transfactor: Transcription factor activity estimation via probabilistic gene expression deconvolution biorxiv.org/content/10.110…

PASTE2 Partial alignment (based on a subset of spots) of multi-slice #SpatialTranscriptomics 3D reconstruction of 16-slide Stereo-seq Drosophila embryo Partial fused Gromov-Wasserstein #OptimalTransport vs PASTE Pamona Tangram Alignment evaluated with Label Transfer

Introducing RAEFISH, our lab's new flagship image-based spatial transcriptomics technology that simultaneously enables single-molecule spatial resolution and whole-genome level coverage of long and short, endogenous and engineered RNA species in cell cultures and intact tissues.

KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors Now KnockTF 2.0 👤🐭🌱🌽 >1400 transcriptomes ~800 TF/TcoF licpathway.net/KnockTF/index.… Go to "Search" for your TF "Quick Search" does not work Nucleic Acids Res 2020

CHOIR is now online Nature Genetics! CHOIR is a new clustering method for single-cell data that evaluates whether clusters represent statistically distinct cell populations. CHOIR scales to millions of cells and works with single-/multi-omic data of any type! nature.com/articles/s4158…

InSituCor: exploring spatially correlated genes conditional on the cell type landscape genomebiology.biomedcentral.com/articles/10.11… 🧬🖥️🧪 github.com/Nanostring-Bio…

🧵5 Top Free Alternatives to BioRender for Scientific Illustrations! These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs. Save and share the post!