Reposted by Mehdi Pirooznia
I've posted the notes/slides for my computational biology class at github.com/pachterlab/B... Topics were chosen based on appearing in >=3 bio areas, although for focus examples are all drawn from #scRNAseq. Homeworks include both theory and exploration of data (via GoogleColab).
September 22, 2023 at 1:55 PM
I've posted the notes/slides for my computational biology class at github.com/pachterlab/B... Topics were chosen based on appearing in >=3 bio areas, although for focus examples are all drawn from #scRNAseq. Homeworks include both theory and exploration of data (via GoogleColab).
Reposted by Mehdi Pirooznia
Required reading by @lpachter.bsky.social. Seurat vs Scanpy processing, and how package versions affect your analysis 👀 www.biorxiv.org/content/10.1...
The impact of package selection and versioning on single-cell RNA-seq analysis
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
April 5, 2024 at 9:21 PM
Required reading by @lpachter.bsky.social. Seurat vs Scanpy processing, and how package versions affect your analysis 👀 www.biorxiv.org/content/10.1...
Reposted by Mehdi Pirooznia
Do you know gget by the Pachter lab? You should! It now includes efficient querying of Bgee in Python. Get high quality curated gene expression data directly in Python or command line. pachterlab.github.io/gget/en/bgee... #RNAseq #biocuration #Python #scRNAseq
gget bgee - gget
gget enables efficient querying of genomic reference databases
pachterlab.github.io
October 3, 2024 at 12:45 PM
Do you know gget by the Pachter lab? You should! It now includes efficient querying of Bgee in Python. Get high quality curated gene expression data directly in Python or command line. pachterlab.github.io/gget/en/bgee... #RNAseq #biocuration #Python #scRNAseq
Reposted by Mehdi Pirooznia
Pan-Cancer Drug Sensitivity Prediction from Gene Expression using Deep Learning https://www.biorxiv.org/content/10.1101/2024.11.15.623715v1
Pan-Cancer Drug Sensitivity Prediction from Gene Expression using Deep Learning https://www.biorxiv.org/content/10.1101/2024.11.15.623715v1
Cancer is a group of complex diseases, with tumor heterogeneity, durable drug efficacy, emerging res
www.biorxiv.org
November 16, 2024 at 5:47 AM
Pan-Cancer Drug Sensitivity Prediction from Gene Expression using Deep Learning https://www.biorxiv.org/content/10.1101/2024.11.15.623715v1
Orthrus: an AI-powered, cloud-ready, and open-source hybrid approach for metaproteomics https://www.biorxiv.org/content/10.1101/2024.11.15.623814v1
Orthrus: an AI-powered, cloud-ready, and open-source hybrid approach for metaproteomics https://www.biorxiv.org/content/10.1101/2024.11.15.623814v1
While metaproteomics provides invaluable insight into microbial communities and functions, significa
www.biorxiv.org
November 16, 2024 at 3:09 PM
Pan-Cancer Drug Sensitivity Prediction from Gene Expression using Deep Learning https://www.biorxiv.org/content/10.1101/2024.11.15.623715v1
Pan-Cancer Drug Sensitivity Prediction from Gene Expression using Deep Learning https://www.biorxiv.org/content/10.1101/2024.11.15.623715v1
Cancer is a group of complex diseases, with tumor heterogeneity, durable drug efficacy, emerging res
www.biorxiv.org
November 16, 2024 at 3:09 PM
A comprehensive human embryo reference tool using single-cell RNA-sequencing data. #SingleCell #scRNAseq #HumanEmbryo #ReferenceDataSet #NatureMethods #BioSky #SciSky 🧪
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A comprehensive human embryo reference tool using single-cell RNA-sequencing data - Nature Methods
This resource integrates different human embryo datasets to create a transcriptional reference map of human embryonic development from zygote to gastrula.
www.nature.com
November 16, 2024 at 3:08 PM
Reposted by Mehdi Pirooznia
Super excited about this cell typing collab between 10x Genomics and the Broad. broad.io/CAS-News
Try it for free on cloud.10xgenomics.com/cloud-analysis and look out for more in the next Cell Ranger release coming imminently ;) (Let us know what you think!)
#singlecell #bioinformatics #genomics
November 15, 2024 at 4:16 PM
Super excited about this cell typing collab between 10x Genomics and the Broad. broad.io/CAS-News
Try it for free on cloud.10xgenomics.com/cloud-analysis and look out for more in the next Cell Ranger release coming imminently ;) (Let us know what you think!)
#singlecell #bioinformatics #genomics
Can AI review the scientific literature — and figure out what it all means? Artificial intelligence could help speedily summarize research. But it comes with risks.
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Can AI review the scientific literature — and figure out what it all means?
Artificial intelligence could help speedily summarize research. But it comes with risks.
www.nature.com
November 15, 2024 at 1:33 AM
Can AI review the scientific literature — and figure out what it all means? Artificial intelligence could help speedily summarize research. But it comes with risks.
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Mehdi Pirooznia
Weekly Recap: agentic multiomic analysis, metagenome profiling, GWAS beyond SNPs, private information leakage from scRNA-seq, unlearning viral knowledge for safe protein language models, biosecurity, scRNA-seq copilot, #Rstats for biomarker analysis, ... blog.stephenturner.us/p/weekly-rec...
Weekly Recap (Nov 2024, part 2)
What I'm reading in agentic multiomic analysis, metagenome profiling, GWAS beyond SNPs, private information leakage from scRNA-seq, unlearning viral knowledge for safe protein language models, ...
blog.stephenturner.us
November 15, 2024 at 12:17 AM
Weekly Recap: agentic multiomic analysis, metagenome profiling, GWAS beyond SNPs, private information leakage from scRNA-seq, unlearning viral knowledge for safe protein language models, biosecurity, scRNA-seq copilot, #Rstats for biomarker analysis, ... blog.stephenturner.us/p/weekly-rec...