RT @yusufroohani: scBaseCamp was built by directly mining all publicly accessible 10X Genomics scRNAseq data from the Sequence Read Archive….

DeepCellTypes pre-print: Code and vignettes:

Thank you @xuefei_w (@davidvanvalen lab) for a great presentation of DeepCellTypes at our NYU Single-Cell Club. DeepCellTypes is a spatial proteomics phenotyping method with the ability to generalize across diverse datasets with varying marker panels.

RT @naturemethods: The wait is over!! We are thrilled to announce that we have chosen Spatial Proteomics as 2024’s Method of the Year! 🥳. F….

RT @simonduerr: This is great! @NIAIDNews have launched a collection of public domain illustrations (currently 550 individual icons) https:….

TCAT pre-print: Code and vignettes:

Thank you @DKotliar (@soumya_boston lab) for a great presentation of CellAnnoTator (*CAT) and T-CellAnnoTator (TCAT) at our NYU Single-Cell Club. TCAT annotates scRNA-Seq T-cell subsets with predefined gene expression programs compiled from a range of reference datasets.

RT @BockLab: 🗨️ WANNA TALK TO YOUR CELLS? Try out CellWhisperer – our new multimodal AI that turns single-cell RNA-seq analysis into a conv….

RT @LGMartelotto: Here we go…repurposing spatial imaging techs to achieve ultra-low to ultra-high, multiplexing, nuclei, cells, single (RNA….

RT @const_ae: There's a lot of excitement about foundation models and their ability to learn biology 🧬💻. But current tools for perturbation….

RT @St_Megas: Are you missing cells and cell types in your single-cell multiome experiments @10xGenomics? Check out EmptyDropsMultiome @Mar….

RT @MarketCurrents: $ILMN - Illumina buys Fluent Biosciences to accelerate single-cell analysis

RT @asharmaiisc: Systematic comparison of sequencing-based spatial transcriptomic methods in @naturemethods . In summary:.“- Stereo-seq, Sl….

CellChat v2 pre-print: Code and vignettes:

Thank you @suoqin_jin for a great presentation of CellChat at our NYU Single-Cell Club. CellChat v2 expands the underlying CellChatDB database, extends the inference of cell-cell communication to spatially-resolved datasets, and adds an interactive browser for output exploration.

Seems like you can determine sequencing platform from the quality scores alone using a GPT model

RT @david_van_dijk:

RT @assaron: I'm happy to share that out paper on Phantasus, a web-application for visual and interactive gene expression analysis, got out….

VeloCycle pre-print: Code and vignettes:

Thank you @alexlederer19 (@GioeleLaManno lab) for a great presentation of VeloCycle at our NYU Single-Cell Club. VeloCycle is a new implementation of RNA velocity that combines velocity field and manifold estimation, tailored for the cell cycle.