Gyan Prakash Mishra, PhD

Postdoc @WUSTL #ComputationalBiology #Neuroscience Past : @UTSWBrain @DBT_ILS @csir_iicb @NIPER_Kolkata @MAHE_Manipal

[Gyan Prakash Mishra, PhD @gprakash047]

Detection of intra-host SNV frequency in SARS-CoV-2 genome survellience, a method to understand spatio-temporal dynamics of virus evolution.

🧵..Highlighting the results of our study published in @NAR_Open

Congrats and Thanks to all the co-authors.

[ankit @pxthxk]

Our paper discussing the spatio-temporal dynamics of SARS-CoV-2 intra-host variability is now up on Nucleic Acids Research.

@IGIBSocial @mukerjim @imgsb

https://t.co/p1TxFsNRrK

[Stephen Turner 🦋 @stephenturner.us @strnr]

Low overlap of transcription factor DNA binding and regulatory targets https://t.co/SGUFa0kG7p (read free: https://t.co/1DAs2K1elT) 🧬🖥️🧪

[Stephen Turner 🦋 @stephenturner.us @strnr]

xOmicsShiny: an R shiny application for cross-omics data analysis and pathway mapping https://t.co/p5Tl02nvKb #Rstats 🧬🖥️🧪 https://t.co/toGgEsYArx

[Xueyi Dong 董雪漪 @DongXueyi]

edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets https://t.co/IPiHI5IPAg

[Stephen Turner 🦋 @stephenturner.us @strnr]

The current landscape and emerging challenges of benchmarking single-cell methods https://t.co/sB9LdfVRIn 🧬🖥️🧪 https://t.co/xsxCQQ45Zg

[Hiroshi Ochiai @Hiro_Ochiai_En]

🚨 Exciting news! 🚨
Our latest paper is now published in Science Advances! 🎉
"Transcription-coupled changes in genomic region proximities during transcriptional bursting"
👉 Read it here: https://t.co/FT3bJq5bXq

[UTSWPostdocOffice @UTSWPostdocs]

@utswpda #postdocs get together for an ice cream sundae party Mon. Nov. 18th at 4pm in the Bryan Williams Student Center Lounge.

[Stephen Turner 🦋 @stephenturner.us @strnr]

PCBS: An R package for fast and accurate analysis of bisulfite sequencing data https://t.co/HnVKiapn9a 🧬🖥️ #rstats https://t.co/LUmnr1EBxK

[Stephen Turner 🦋 @stephenturner.us @strnr]

After getting duckpilled and writing yesterday about DuckDB and duckplyr as a faster alternative to base R and dplyr, today I follow that up with a look at parquet (nanoparquet) as a better and faster alternative to CSV (readr) https://t.co/0juNCapsiV #rstats

[Stephen Turner 🦋 @stephenturner.us @strnr]

CleanUpRNAseq: An R/Bioconductor Package for Detecting and Correcting DNA Contamination in RNA-Seq Data https://t.co/BqvZvh3cCn #Rstats https://t.co/PlDhkt5uQ3 🧬🖥️ https://t.co/uyZpf4tMsb

[Ming "Tommy" Tang @tangming2005]

The tidyCoverage R package provides a framework for rapid investigation of collections of genomic tracks over genomic features, relying on the principle of tidy data manipulation https://t.co/dI7fvIuJjI

[Gyan Prakash Mishra, PhD @gprakash047]

@sudhirthakurela @generegulation @AllAboutTFs @ChromatinHaiku do you think the super Enhancer could fit into this timeline, i know there are different views.
https://t.co/5TYlCEOnTU

[Zuguang Gu | 顾祖光 @jokergoo_gu]

My new manuscript on citation analysis: Two separated worlds - on the international influence of life science and biomedical research

https://t.co/zm5659oQtO

[Paolo Di Tommaso @PaoloDiTommaso]

Just uploaded a small plugin to execute GPT prompts in Nextflow scripts and collect the response in form of structured data for downstream analysis. Hope you will find it useful! ✨✨
https://t.co/ai8KcnKdcw

[Stephen Turner 🦋 @stephenturner.us @strnr]

Google's new scholar PDF reader extension is great. In-text citations are previewable links to references, clickable TOC headings, figure/table references. https://t.co/1HngAntGaE

[𝕐 @nomad421]

Reading "Comparative evaluation of full-length isoform quantification from RNA-Seq"

https://t.co/Y9K6NQsbBq

[Gyan Prakash Mishra, PhD @gprakash047]

@senergystic @sudhirthakurela you can check this paper https://t.co/gOjECoDsvB.1126/science.1086446

[Gyan Prakash Mishra, PhD @gprakash047]

This is from public datasets, gene name formatted as dates.
Take home : do not save datasets with gene name in excel.

[Lior Pachter @lpachter]

The edgeR differential analysis tool has been updated to version 4.0., and this update features support for isoform-level DE, which is important functionality that can be used for #scRNAseq (via pseudobulk). Great to see that transcript-level analysis has become mainstream. 1/🧵

[Gyan Prakash Mishra, PhD @gprakash047]

@HamidGhanadan @ShahramSN i guess you mean cytosine

[Hajk-Georg Drost @HajkDrost]

Data retrieval for massive (comparative) genomics is not easy, especially when you care about genome origin, assembly quality & functional annotation.

We hope new release {biomartr} v1.0.5 will help you to automate retrieval & reproducibility at scale ⏩⏩https://t.co/VPy4fYMOsb