Bioinformatics can be fun, but with multiple steps and dependencies, things can get complex fast. And then the despair. How did I generate this intermediate file? What parameters did I use to run this script? Anxiety The solution: A workflow manager A 🧵 on how to get started

Complex heatmap visualization, created by Zuguang Gu | 顾祖光 ComplexHeatmap provides the richest toolset for constructing highly customizable heatmaps, easily establishing connections between multisource information. #Bioinformatics #R #visualization onlinelibrary.wiley.com/doi/10.1002/im…

I am thrilled to share that our paper is now published in Nature Biotechnology!. Many thanks to all people involved in the work Prof Tony Papenfuss Momeneh Foroutan TranslationalGenomic. WEHI (Walter and Eliza Hall Institute) nature.com/articles/s4158….

How do gene regulatory networks controlling hormone response vary in time and space? In our latest work doi.org/10.1101/2022.0… we use time-series scRNA-seq to profile brassinosteroid response across cell types and development stages of the Arabidopsis root

SpaceX: Gene Co-expression Network Estimation for Spatial Transcriptomics academic.oup.com/bioinformatics…

SHAP is a good feature attribution algo BUT it identifies wrong features even in linear regression. Our #NeurIPS2022 paper finds where SHAP goes wrong and proposes a simple fix *WeightedSHAP* that greatly improves attribution arxiv.org/pdf/2209.13429… Code: github.com/ykwon0407/Weig…

We're excited to share our most recent article, which has been accepted by eLife - the journal. From the lab of Debojyoti Chakraborty CSIR-IGIB, my colleague asgar hussain ansari and I sought to expand CRISPR-based SNV detection by means of an assay-designing web server, CriSNPr.🕵🏽‍♂️ elifesciences.org/articles/77976

Today we report in eLife - the journal a webserver for curated and de-novo design of sgRNAs for CRISPRdx applications. This work was the brainchild of asgar hussain ansari and ꪑꪖꪀꪮ꠹ ᛕꪊꪑꪖ᥅ 🤓| and supported extensively by Sajal Sarkar. elifesciences.org/articles/77976 (1/n) souvik

There was little online material to learn bioinformatics 10 years ago when I started. I curated ten resources to learn bioinformatics for FREE 🧵👇

This is pretty slick — query with an accession and directly download actual read files (with preference for SRA or ENA) directly in Robert A. Petit III, PhD's fastq-dl github.com/rpetit3/fastq-…; all wrapped up in a nice "rich" interface :).

SpliceTools, a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing. #RNAsplicing #AlternativeSplicing #Bioinformatics @NAR_Open academic.oup.com/nar/advance-ar…

Looking for #Bioinformatics courses on #GitHub? 🧐 You're in luck! 🍀Yann Haefliger Patricia Palagi - Hope for better 🇧🇷 🚩🌟! and I from SIB have created #Glittr (glittr.org): a webapp that helps you find and compare awesome training materials. 🎉 How does it work? And how can you join us? Read on! 👇

UMAP/tSNE suffers from overplotting, lack of quantitative information, and distort global and local distance relative to the original high-dimensional space. scBubbletree promotes simple and transparent visual exploration of scRNA-seq data. R package: bioconductor.org/packages/relea…

Interested in single cell genomics but need help getting started? Check out the full agenda for our Single Cell Genomics Day next Friday (4/7). All talks will be live-streamed (no registration required) at satijalab.org/scgd23

Although the thesis examiner said that asgar hussain ansari can be given two doctorate degrees, we'll settle with one. Congratulations Dr. Ansari, it was a pleasure having you around in the lab, well done! CSIR-IGIB

Debojyoti Chakraborty asgar hussain ansari CSIR-IGIB So well deserved, congratulations asgar hussain ansari

A comparative analysis of 16S classification pipelines+databases: - Kraken 2 and Pathoscope2 perform better compared to DADA2 and QIIME 2 - In terms of reference libraries, SILVA & RefSeq/Kraken 2 libraries were more accurate than Greengenes. nature.com/articles/s4159…

Whole genomic analysis reveals atypical non-homologous off-target large structural variants induced by CRISPR-Cas9-mediated genome editing. #GenomeAnalysis #CRISPR_Cas9 #StructuralVariantsCreation Nature Communications nature.com/articles/s4146…

BioConvert: a comprehensive format converter for life sciences. #FormatConversion #DataFormats #Bioinformatics #NARgenomicsAndBioinformatics academic.oup.com/nargab/article…

BRAKER3: Fully Automated Genome Annotation Using RNA-Seq and Protein Evidence with GeneMark-ETP, AUGUSTUS and TSEBRA. #GenomeAnnotation #RNAseq bioRxiv biorxiv.org/content/10.110…