#singlecell — Public Fediverse posts

Pipeline release! nf-core/pixelator v5.0.1 - nf-core/pixelator 5.0.1!
Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/5.0.1

#molecularpixelation #pixelator #pixelgentechnologies #proteins #singlecell #singlecellomics #nfcore #openscience #nextflow #bioinformatics

#Bioinformatics
#Genomics
#Genetics
#RStats

I'm fed up. I've been working on multiple projects for other people. Constantly context switching. Slowly moving forward because they're separate projects that are related to grants due at essentially the same time.

I need to do #SingleCell trajectory analysis. I had solved all of the slingshot / tradeSeq execution years ago. *But* before switching to "everything is a project". The code's gone. Poof.

I deleted it to free space at some point. 🤬

Postdoctoral Scholar – Dendritic Cell Biology & Reprogramming, UCSD
University of California San Diego

Join us as a #postdoc in #immunology studying dendritic cells and #cellidentity using #CRISPR and #singlecell genomics at UCSD.

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-california-san-diego-27778-postdoctoral-s...
https://jobrxiv.org/job/university-of-california-san-diego-27778-postdoctoral-scholar-dendritic-cell-biology-reprogramming-ucsd/?fsp_sid=13710

Pipeline release! nf-core/pixelator v5.0.0 - nf-core/pixelator 5.0.0!
Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/5.0.0

#molecularpixelation #pixelator #pixelgentechnologies #proteins #singlecell #singlecellomics #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/scrnaseq v4.2.0 - 4.2.0!
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.2.0

#10xgenomics #10xgenomics #alevin #bustools #cellranger #kallisto #rnaseq #singlecell #starsolo #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mcmicro v2.0.0 - 2.0.0!
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Please see the changelog: https://github.com/nf-core/mcmicro/releases/tag/2.0.0

#bioformats #imageanalysis #imageprocessing #microscopy #multiplexedimaging #ometiff #registration #segmentation #singlecell #spatial #stitching #tma #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/mcmicro v2.0.0 - 2.0.0!
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Please see the changelog: https://github.com/nf-core/mcmicro/releases/tag/2.0.0

#bioformats #imageanalysis #imageprocessing #microscopy #multiplexedimaging #ometiff #registration #segmentation #singlecell #spatial #stitching #tma #nfcore #openscience #nextflow #bioinformatics

6/ Lastly, in https://www.nature.com/articles/s41592-023-02003-w. the observed sensitivity deficits stem from three sources: (1) poor annotation of 3′ gene ends; (2) issues with intronic read incorporation; and (3) gene overlap-derived read loss. #singlecell #RNAseq

Pipeline release! nf-core/scnanoseq v1.3.0 - nf-core/scnanoseq v1.3.0 - Steel Elephant!
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.3.0

#10xgenomics #longreadsequencing #nanopore #rnaseq #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

RE: https://genomic.social/@bgeedb/116760320692467761

Super happy to see this out. 😎 #FAIR #FAIRdata #SingleCell #scRNAseq

Pipeline release! nf-core/pixelator v4.1.2 - nf-core/pixelator 4.1.2!
Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/4.1.2

#molecularpixelation #pixelator #pixelgentechnologies #proteins #singlecell #singlecellomics #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/pixelator v4.1.1 - nf-core/pixelator 4.1.1!
Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/4.1.1

#molecularpixelation #pixelator #pixelgentechnologies #proteins #singlecell #singlecellomics #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/pixelator v4.1.0 - nf-core/pixelator 4.1.0!
Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/4.1.0

#molecularpixelation #pixelator #pixelgentechnologies #proteins #singlecell #singlecellomics #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/pixelator v4.0.0 - nf-core/pixelator 4.0.0!
Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/4.0.0

#molecularpixelation #pixelator #pixelgentechnologies #proteins #singlecell #singlecellomics #nfcore #openscience #nextflow #bioinformatics

Postdoctoral Scholar – Dendritic Cell Biology & Reprogramming, UCSD
University of California San Diego

Join us as a #postdoc in #immunology studying dendritic cells and #cellidentity using #CRISPR and #singlecell genomics at UCSD.

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-california-san-diego-27778-postdoctoral-s...
https://jobrxiv.org/job/university-of-california-san-diego-27778-postdoctoral-scholar-dendritic-cell-biology-reprogramming-ucsd/?fsp_sid=11833

Postdoc in Single-Cell and Spatial Multi-Omic Gene Regulatory Networks
UMass Chan Medical School

Decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference and #MachineLearning as a #postdoc! No biomed bg needed.

See the full job description on jobRxiv: https://jobrxiv.org/job/umass-chan-medical-school-27778-postdoc-in-single-cel...
https://jobrxiv.org/job/umass-chan-medical-school-27778-postdoc-in-single-cell-and-spatial-multi-omic-gene-regulatory-networks/?fsp_sid=11689

Postdoctoral Scholar – Dendritic Cell Biology & Reprogramming, UCSD
University of California San Diego

Join us as a #postdoc in #immunology studying dendritic cells and #cellidentity using #CRISPR and #singlecell genomics at UCSD.

See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-california-san-diego-27778-postdoctoral-s...
https://jobrxiv.org/job/university-of-california-san-diego-27778-postdoctoral-scholar-dendritic-cell-biology-reprogramming-ucsd/?fsp_sid=11497

Postdoc in Single-Cell and Spatial Multi-Omic Gene Regulatory Networks
UMass Chan Medical School

Decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference and #MachineLearning as a #postdoc! No biomed bg needed.

See the full job description on jobRxiv: https://jobrxiv.org/job/umass-chan-medical-school-27778-postdoc-in-single-cel...
https://jobrxiv.org/job/umass-chan-medical-school-27778-postdoc-in-single-cell-and-spatial-multi-omic-gene-regulatory-networks/?fsp_sid=11057

Postdoc in Single-Cell and Spatial Multi-Omic Gene Regulatory Networks
UMass Chan Medical School

Decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference and #MachineLearning as a #postdoc! No biomed bg needed.

See the full job description on jobRxiv: https://jobrxiv.org/job/umass-chan-medical-school-27778-postdoc-in-single-cel...
https://jobrxiv.org/job/umass-chan-medical-school-27778-postdoc-in-single-cell-and-spatial-multi-omic-gene-regulatory-networks/?fsp_sid=11049

🤯 What if most “biological insights” are just mixed-up signals we never untangled?

🔗 Integrative Learning of Disentangled Representations from Single-Cell RNA-Sequencing Datasets. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0015

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#SystemsBiology #Genomics #Bioinformatics #ComputationalBiology #AIinBiology #SingleCell #MachineLearning #DataScience #LifeSciences

🧬 Can we map the cascade of gene activity that guides cells through differentiation?

🔗 Pseudotimecascade Visualizes Gene Expression Cascade in Pseudotime Analysis. Computational and Structural Biotechnology Journal (CSBJ). https://spj.science.org/doi/epdf/10.34133/csbj.0007

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj

#SingleCell #Genomics #Bioinformatics #SystemsBiology #GeneExpression #ComputationalBiology

[Edit] I think I finally have some winners WITH cell identities, though I had to dig for that part. Thanks!

Anyone working in #Genomics #SingleCell #RNASeq aware of a good data source for human kidney single-cell data that has *labeled* cell types.

We have a #GWAS that the target tissue would be kidneys. I'm stuck doing cell type analyses until I can find some labeled cell type data to connect back to the association data.

Pipeline release! nf-core/scnanoseq v1.2.2 - nf-core/scnanoseq v1.2.2 - Thallium Tiger!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.2.2

#10xgenomics #longreadsequencing #nanopore #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/pixelator v3.0.1 - nf-core/pixelator 3.0.1!
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/3.0.1

#molecularpixelation #pixelator #pixelgentechnologies #proteins #singlecell #singlecellomics #nfcore #openscience #nextflow #bioinformatics

🔬 Spatial Transcriptomics - Feb 2026

• CLIM-TIME maps 7 TME subtypes linked to T cell therapy response
• Kupffer cells promote immune evasion in liver metastases
• CD276 drives chemoresistance in pancreatic cancer
• T cell activation correlates with better survival in glioblastoma
• mFISH3D visualizes multiple mRNA types in intact mouse brains
• RNA-modifying proteins emerge as potential therapeutic targets

https://pir.sh/9XygJ0Xd3w

#SpatialTranscriptomics #CancerBiology #SingleCell #Biology

Pipeline release! nf-core/pixelator v3.0.0 - nf-core/pixelator 3.0.0!
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/3.0.0

#molecularpixelation #pixelator #pixelgentechnologies #proteins #singlecell #singlecellomics #nfcore #openscience #nextflow #bioinformatics

#Genetics #Genomics #Bioinformatics

Anyone have any favorites for R packages to do cell-type classification of #PBMCs in #SingleCell #RNASeq? I've used scGate with manual marker decisions in the past, but it's been a while since I've had to do it so I wasn't sure how the landscape had changed.