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#singlecell

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nf-core<p>Pipeline release! nf-core/scnanoseq v1.2.0 - nf-core/scnanoseq v1.2.0 - Copper Rhinoceros!</p><p>Please see the changelog: <a href="https://github.com/nf-core/scnanoseq/releases/tag/1.2.0" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/nf-core/scnanoseq/r</span><span class="invisible">eleases/tag/1.2.0</span></a></p><p><a href="https://mstdn.science/tags/10xgenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>10xgenomics</span></a> <a href="https://mstdn.science/tags/longreadsequencing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>longreadsequencing</span></a> <a href="https://mstdn.science/tags/nanopore" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nanopore</span></a> <a href="https://mstdn.science/tags/scrnaseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>scrnaseq</span></a> <a href="https://mstdn.science/tags/singlecell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>singlecell</span></a> <a href="https://mstdn.science/tags/nfcore" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nfcore</span></a> <a href="https://mstdn.science/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>openscience</span></a> <a href="https://mstdn.science/tags/nextflow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nextflow</span></a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
Alberto Perez-Posada<p>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! <a href="https://www.science.org/doi/10.1126/sciadv.adm7042" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">science.org/doi/10.1126/sciadv</span><span class="invisible">.adm7042</span></a> <a href="https://genomic.social/tags/singlecell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>singlecell</span></a> <a href="https://genomic.social/tags/scrna" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>scrna</span></a> <a href="https://genomic.social/tags/allometry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>allometry</span></a> <a href="https://genomic.social/tags/splitseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>splitseq</span></a> <a href="https://genomic.social/tags/planarians" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>planarians</span></a> <a href="https://genomic.social/tags/generegulation" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>generegulation</span></a></p>
jobRxiv<p>Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks </p><p>University of Massachusetts Chan Medical School</p><p>Join us to decode <a href="https://mas.to/tags/GeneRegulatoryNetwork" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GeneRegulatoryNetwork</span></a> from <a href="https://mas.to/tags/SingleCell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SingleCell</span></a> multiomics with <a href="https://mas.to/tags/CausalInference" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CausalInference</span></a> as a <a href="https://mas.to/tags/postdoc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>postdoc</span></a>! Quantitative bg needed.</p><p>See the full job description on jobRxiv: <a href="https://jobrxiv.org/job/university-of-massachusetts-chan-medica" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/university-of-</span><span class="invisible">massachusetts-chan-medica</span></a>...<br><a href="https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=94702" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/university-of-</span><span class="invisible">massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=94702</span></a></p>
jobRxiv<p>Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks </p><p>University of Massachusetts Chan Medical School</p><p>Join us to decode <a href="https://mas.to/tags/GeneRegulatoryNetwork" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GeneRegulatoryNetwork</span></a> from <a href="https://mas.to/tags/SingleCell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SingleCell</span></a> multiomics with <a href="https://mas.to/tags/CausalInference" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CausalInference</span></a> as a <a href="https://mas.to/tags/postdoc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>postdoc</span></a>! Quantitative bg needed.</p><p>See the full job description on jobRxiv: <a href="https://jobrxiv.org/job/university-of-massachusetts-chan-medica" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/university-of-</span><span class="invisible">massachusetts-chan-medica</span></a>...<br><a href="https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=94125" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/university-of-</span><span class="invisible">massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=94125</span></a></p>
jobRxiv<p>Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks </p><p>University of Massachusetts Chan Medical School</p><p>Join us to decode <a href="https://mas.to/tags/GeneRegulatoryNetwork" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GeneRegulatoryNetwork</span></a> from <a href="https://mas.to/tags/SingleCell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SingleCell</span></a> multiomics with <a href="https://mas.to/tags/CausalInference" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CausalInference</span></a> as a <a href="https://mas.to/tags/postdoc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>postdoc</span></a>! Quantitative bg needed.</p><p>See the full job description on jobRxiv: <a href="https://jobrxiv.org/job/university-of-massachusetts-chan-medica" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/university-of-</span><span class="invisible">massachusetts-chan-medica</span></a>...<br><a href="https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=93671" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/university-of-</span><span class="invisible">massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=93671</span></a></p>
jobRxiv<p>Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks </p><p>University of Massachusetts Chan Medical School</p><p>Join us to decode <a href="https://mas.to/tags/GeneRegulatoryNetwork" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GeneRegulatoryNetwork</span></a> from <a href="https://mas.to/tags/SingleCell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SingleCell</span></a> multiomics with <a href="https://mas.to/tags/CausalInference" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CausalInference</span></a> as a <a href="https://mas.to/tags/postdoc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>postdoc</span></a>! Quantitative bg needed.</p><p>See the full job description on jobRxiv: <a href="https://jobrxiv.org/job/university-of-massachusetts-chan-medica" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/university-of-</span><span class="invisible">massachusetts-chan-medica</span></a>...<br><a href="https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=93482" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/university-of-</span><span class="invisible">massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=93482</span></a></p>
jobRxiv<p>Postdoc in Single-Cell Multi-Omic Gene Regulatory Networks </p><p>University of Massachusetts Chan Medical School</p><p>Join us to decode <a href="https://mas.to/tags/GeneRegulatoryNetwork" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GeneRegulatoryNetwork</span></a> from <a href="https://mas.to/tags/SingleCell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SingleCell</span></a> multiomics with <a href="https://mas.to/tags/CausalInference" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CausalInference</span></a> as a <a href="https://mas.to/tags/postdoc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>postdoc</span></a>! Quantitative bg needed.</p><p>See the full job description on jobRxiv: <a href="https://jobrxiv.org/job/university-of-massachusetts-chan-medica" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/university-of-</span><span class="invisible">massachusetts-chan-medica</span></a>...<br><a href="https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=93328" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/university-of-</span><span class="invisible">massachusetts-chan-medical-school-27778-postdoc-in-single-cell-multi-omic-gene-regulatory-networks/?feed_id=93328</span></a></p>
nf-core<p>Pipeline release! nf-core/scnanoseq v1.1.0 - nf-core/scnanoseq v1.1.0 - Iron Alligator!</p><p>Please see the changelog: <a href="https://github.com/nf-core/scnanoseq/releases/tag/1.1.0" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/nf-core/scnanoseq/r</span><span class="invisible">eleases/tag/1.1.0</span></a></p><p><a href="https://mstdn.science/tags/10xgenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>10xgenomics</span></a> <a href="https://mstdn.science/tags/longreadsequencing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>longreadsequencing</span></a> <a href="https://mstdn.science/tags/nanopore" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nanopore</span></a> <a href="https://mstdn.science/tags/scrnaseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>scrnaseq</span></a> <a href="https://mstdn.science/tags/singlecell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>singlecell</span></a> <a href="https://mstdn.science/tags/nfcore" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nfcore</span></a> <a href="https://mstdn.science/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>openscience</span></a> <a href="https://mstdn.science/tags/nextflow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nextflow</span></a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
nf-core<p>Pipeline release! nf-core/scrnaseq v4.0.0 - 4.0.0!</p><p>Please see the changelog: <a href="https://github.com/nf-core/scrnaseq/releases/tag/4.0.0" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/nf-core/scrnaseq/re</span><span class="invisible">leases/tag/4.0.0</span></a></p><p><a href="https://mstdn.science/tags/10xgenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>10xgenomics</span></a> <a href="https://mstdn.science/tags/10xgenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>10xgenomics</span></a> <a href="https://mstdn.science/tags/alevin" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>alevin</span></a> <a href="https://mstdn.science/tags/bustools" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bustools</span></a> <a href="https://mstdn.science/tags/cellranger" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>cellranger</span></a> <a href="https://mstdn.science/tags/kallisto" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>kallisto</span></a> <a href="https://mstdn.science/tags/rnaseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>rnaseq</span></a> <a href="https://mstdn.science/tags/singlecell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>singlecell</span></a> <a href="https://mstdn.science/tags/starsolo" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>starsolo</span></a> <a href="https://mstdn.science/tags/nfcore" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nfcore</span></a> <a href="https://mstdn.science/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>openscience</span></a> <a href="https://mstdn.science/tags/nextflow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nextflow</span></a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
nf-core<p>Pipeline release! nf-core/molkart v1.1.0 - 1.1.0 - Resolution Road!</p><p>Please see the changelog: <a href="https://github.com/nf-core/molkart/releases/tag/1.1.0" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/nf-core/molkart/rel</span><span class="invisible">eases/tag/1.1.0</span></a></p><p><a href="https://mstdn.science/tags/fish" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>fish</span></a> <a href="https://mstdn.science/tags/imageprocessing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>imageprocessing</span></a> <a href="https://mstdn.science/tags/imaging" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>imaging</span></a> <a href="https://mstdn.science/tags/molecularcartography" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>molecularcartography</span></a> <a href="https://mstdn.science/tags/segmentation" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>segmentation</span></a> <a href="https://mstdn.science/tags/singlecell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>singlecell</span></a> <a href="https://mstdn.science/tags/spatial" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>spatial</span></a> <a href="https://mstdn.science/tags/transcriptomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>transcriptomics</span></a> <a href="https://mstdn.science/tags/nfcore" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nfcore</span></a> <a href="https://mstdn.science/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>openscience</span></a> <a href="https://mstdn.science/tags/nextflow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nextflow</span></a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
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Ming 'Tommy' Tang

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 divingintogeneticsandgenomics.

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.
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Eli Roberson (he/him)

#Genomics #SingleCell

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.

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