Happy to see out our latest work on studying animal body size variations using single cell transcriptomics to measure gene expression of individual cells. Learned my fair bit of statistics here, and most importantly I learned how to build wrapper functions for "complex" tasks in R (such as differntial gene expression) in a modular way. Thanks to all the authors involved! https://www.science.org/doi/10.1126/sciadv.adm7042 #singlecell #scrna #allometry #splitseq #planarians #generegulation
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Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks
University of Massachusetts Chan Medical School
Join us to decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference as a #postdoc! Quantitative bg needed.
See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-massachusetts-chan-medica...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=94702
jobRxiv · Science Jobs - Find science and research jobsThe international job board for scientists, by scientists. Find science jobs in academia or industry: MSc, PhD, Postdoc, Scientist, Faculty and more!
Zooming In—One Cell at a Time!
The 5th Danish #Single-Cell #Symposium is coming to #Copenhagen, and it's THE place to be if you’re into all things single-cell!
Topics will include:
Advances in single-cell #genomics and #transcriptomics
#Computational approaches to #dataanalysis
Applications in health and disease
May 15–16
Hosted at Panum, UCPH
Scientists, students, and techies are all welcome!
Check it out: https://events.au.dk/5thdanishsingle-cellsymposium
Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks
University of Massachusetts Chan Medical School
Join us to decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference as a #postdoc! Quantitative bg needed.
See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-massachusetts-chan-medica...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=94125
jobRxiv · Science Jobs - Find science and research jobsThe international job board for scientists, by scientists. Find science jobs in academia or industry: MSc, PhD, Postdoc, Scientist, Faculty and more!
Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks
University of Massachusetts Chan Medical School
Join us to decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference as a #postdoc! Quantitative bg needed.
See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-massachusetts-chan-medica...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=93671
jobRxiv · Science Jobs - Find science and research jobsThe international job board for scientists, by scientists. Find science jobs in academia or industry: MSc, PhD, Postdoc, Scientist, Faculty and more!
Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks
University of Massachusetts Chan Medical School
Join us to decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference as a #postdoc! Quantitative bg needed.
See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-massachusetts-chan-medica...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=93482
jobRxiv · Science Jobs - Find science and research jobsThe international job board for scientists, by scientists. Find science jobs in academia or industry: MSc, PhD, Postdoc, Scientist, Faculty and more!
Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks
University of Massachusetts Chan Medical School
Join us to decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference as a #postdoc! Quantitative bg needed.
See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-massachusetts-chan-medica...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=93328
jobRxiv · Science Jobs - Find science and research jobsThe international job board for scientists, by scientists. Find science jobs in academia or industry: MSc, PhD, Postdoc, Scientist, Faculty and more!
Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks
University of Massachusetts Chan Medical School
Join us to decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference as a #postdoc! Quantitative bg needed.
See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-massachusetts-chan-medica...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=92866
jobRxiv · Science Jobs - Find science and research jobsThe international job board for scientists, by scientists. Find science jobs in academia or industry: MSc, PhD, Postdoc, Scientist, Faculty and more!
Continued thread
Not much time left to submit an abstract for the #bc2basel conference!
Make sure to apply to be considered for an oral or poster presentation in #MachineLearning, #PrecisionMedicine, #protein3D, #singlecell, #immuneprocesses, or #ecology & #evolution
Submit here: https://tinyurl.com/49w6wthj
Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks
University of Massachusetts Chan Medical School
Join us to decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference as a #postdoc! Quantitative bg needed.
See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-massachusetts-chan-medica...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=92495
jobRxiv · Science Jobs - Find science and research jobsThe international job board for scientists, by scientists. Find science jobs in academia or industry: MSc, PhD, Postdoc, Scientist, Faculty and more!
Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks
University of Massachusetts Chan Medical School
Join us to decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference as a #postdoc! Quantitative bg needed.
See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-massachusetts-chan-medica...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=92012
jobRxiv · Science Jobs - Find science and research jobsThe international job board for scientists, by scientists. Find science jobs in academia or industry: MSc, PhD, Postdoc, Scientist, Faculty and more!
Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks
University of Massachusetts Chan Medical School
Join us to decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference as a #postdoc! Quantitative bg needed.
See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-massachusetts-chan-medica...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=91669
jobRxiv · Science Jobs - Find science and research jobsThe international job board for scientists, by scientists. Find science jobs in academia or industry: MSc, PhD, Postdoc, Scientist, Faculty and more!
Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks
University of Massachusetts Chan Medical School
Join us to decode #GeneRegulatoryNetwork from #SingleCell multiomics with #CausalInference as a #postdoc! Quantitative bg needed.
See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-massachusetts-chan-medica...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=91620
jobRxiv · Science Jobs - Find science and research jobsThe international job board for scientists, by scientists. Find science jobs in academia or industry: MSc, PhD, Postdoc, Scientist, Faculty and more!
Long somatic DNA-repeat expansion drives neurodegeneration in Huntington’s disease.
#HuntingtonsDisease #CAGrepeat #SomaticExpansion #SingleCell
https://www.cell.com/cell/fulltext/S0092-8674(24)01379-5
Replied in thread
8/ Objects make it easy to organize and understand all the data we need for analysis! Just like your body and phone organize the things inside them. #OOP #Bioinformatics #SingleCell #Seurat read my blog post on a simple example in R https://divingintogeneticsandgenomics.com/post/s3-and-s4-objects-in-r-explained/
Chatomics · S3 and S4 objects in R explained | ChatomicsIn R, S3 and S4 objects are related to object-oriented programming (OOP), which allows you to create custom data structures with associated behaviors and methods. Let me explain them using simple language and metaphors, along with practical examples.
S3 Objects Imagine you have a collection of toys, like cars, dolls, and action figures. Each toy has its own set of properties (color, size, material) and behaviors (move, make sounds, etc.
These FASTQ files are driving me batty.
I have FASTQ files for a Chromium prepared library. I run cutadapt to try and limit bad reads. I run RNASTAR solo with correct parameters to extract the read UMI and GEM barcode into UM CB tags of BAM file.
I run umitools to dedup based on barcode.
AssertionError: not all umis are the same length(!): 1 - 10
Why. Is umitools. Dying??? All the barcodes and UMIs should be the same length. They're fixed length pulls from the read.
MATES: a deep learning-based model for locus-specific quantification of transposable elements in single cell.
#Transposons #TEs #SingleCell #Bioinformatics
https://www.nature.com/articles/s41467-024-53114-7
NatureMATES: a deep learning-based model for locus-specific quantification of transposable elements in single cell - Nature CommunicationsTransposable elements (TEs) pose challenges for quantification due to multi-mapping reads. Here, authors present MATES, a deep learning method that accurately assigns reads to specific TE loci, enhancing TE quantification in single-cell omics datasets and identifying marker TEs in cell populations.
Any #rstats #Genomics #SingleCell people used scSplit for genetic demultiplexing of non-hashed mixed samples?
On the GitHub page it says:
"If necessary, remove duplicated reads based on UMI using tools like rmdup in UMI-tools."
https://github.com/jon-xu/scSplit
That makes sense. But shouldn't it really be by GEM *and* UMI? Just UMI would mix GEMs, and that would exclude identically mapping reads from different droplets. Unless umitools checks *both*. I've only used it on fastq files before, not BAM.
GitHubGitHub - jon-xu/scSplit: Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population.Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population. - jon-xu/scSplit
Hey #genomics / #bioinformatics / #SpatialBio world! Any examples of successfully integrating custom count norm methods into a Seurat pipeline for #singlecell data? I’m trying to introduce cell area-based normalization for spatial data but I keep getting strange errors from RunUMAP/uwot 
Pleased to share a review I contributed to, now published in Nature Neuroscience: Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system.
The article highlights how lineage tracing sheds light on cell fate decisions and molecular mechanisms in development and disease. Read here: https://doi.org/10.1038/s41593-024-01827-9