Gaurav Kumar, PhD

Bioinformatics Leader; AI in Life Sciences

[Gaurav Kumar, PhD @Gkbioinfo]

We built Cellxgene Explorer, an open-source app to explore and analyze Cellxgene datasets in seconds, with results at both the single-cell and patient/donor levels.
GitHub: https://t.co/qNBTHUlOyn

#SingleCellRNAseq #scRNAseq #Bioinformatics #ComputationalBiology #Cellxgene

[Gaurav Kumar, PhD @Gkbioinfo]

https://t.co/qNBTHUlOyn

[Gaurav Kumar, PhD @Gkbioinfo]

@MelanieH_L You can use ‘Galaxy’- it’s a very powerful and free tool. Here’s a detailed tutorial with appropriate links embedded. Happy analyzing 🙂 https://t.co/uaJ50lQukh

[Gaurav Kumar, PhD @Gkbioinfo]

‘Enhancedvolcano’ is one of best libraries out there to generate Volcano plots- thanks @KevinBlighe for such a simple method @bioinfblogs @bioinfo_papers

[Gaurav Kumar, PhD @Gkbioinfo]

@AHS_Warranty says ‘the warranty does not control the production of parts’- to which my response is ‘non-service doesn’t control the payment of premiums’. Please refund my premiums from last 3 months and I shouldn’t be paying any addtnl premiums until the issue is resolved.

[Gaurav Kumar, PhD @Gkbioinfo]

@AHS_Warranty 2) no service order should take 3 months to be fixed. This is sheer frustrating that after spending good amount of money on the premiums you still don’t get proper service. If you can’t obtain a part in 3 months provide a replacement unit.

[Gaurav Kumar, PhD @Gkbioinfo]

Okay, so after long wait I decided to escalate this myself @AHS_Warranty. I’ve been waiting a service for my refrigerator since April and there has not been any resolution yet. @AHS_Warranty nobody should wait this much time to get an appliance fixed.

[Gaurav Kumar, PhD @Gkbioinfo]

@AHS_Warranty Then after 2 months they said tech has to call the parts department again for authorization. He called in back on June 21 and the part is not yet received by the tech. My issues are: 1) why I had to call in for the updates, this is your job to stay on the top of the issue.

[Gaurav Kumar, PhD @Gkbioinfo]

@AHS_Warranty Okay- I just sent you a message with the contract number associated with the issue and the detailed issue.

[Gaurav Kumar, PhD @Gkbioinfo]

@AHS_Warranty Obviously you don’t expect me to release my personal information here. There has been a request from the assigned tech for a part which is never been processed by your parts department. It’s been 3 months.

[Gaurav Kumar, PhD @Gkbioinfo]

@SethBlackshaw Just because sequencing technologies can generate false positives, validation method like qRT-PCR is always recommended. If reviewers are asking for validation only on a specific cell type- flow sorting can be done to isolate the specific population followed by qRT-PCR.

[Gaurav Kumar, PhD @Gkbioinfo]

@kischober @Jarosch_S @elisarosix @PGTimmune We also use CD3D/E expression for T-cells. CITE-seq is expensive and takes pretty long time to optimize. Having scTCR repertoire from same cells and integrate the data into scRNAseq would provide the necessary information.

[Gaurav Kumar, PhD @Gkbioinfo]

New member in the house #huskies

[Gaurav Kumar, PhD @Gkbioinfo]

So, my 6 years old suddenly started understanding (and hysterically laughing on the fart jokes)… right time for father and son bonding 😛😛

[Gaurav Kumar, PhD @Gkbioinfo]

Here’s the preprint of our recent study, where we implemented multimodal approaches to identify molecular signature that can predict immunotherapy response when traditional markers are not sufficient

[bioRxiv @biorxivpreprint]

Multimodal genomic markers predict immunotherapy response in the head and neck squamous cell carcinoma https://t.co/VnEMSvMckh #bioRxiv

[Jefferson Research @ResearchAtJeff]

Check out and spread the word on this #JeffersonResearch opportunity!

[Gaurav Kumar, PhD @Gkbioinfo]

This seems pretty promising

[bioRxiv @biorxivpreprint]

Make Interactive Complex Heatmaps in R https://t.co/mfbt9AAAkF #bioRxiv

[Gaurav Kumar, PhD @Gkbioinfo]

Me after realizing that everything on the server is fine, all errors was due to the conda in your path

[Gaurav Kumar, PhD @Gkbioinfo]

This is awesome..thanks for such a nice initiative @satijalab @_hubmap

[Rahul Satija @satijalab]

As part of @_hubmap we're excited to release a web app to automatically map scRNA-seq datasets to four organs, with more to come!

Just upload a gene expression matrix and hit 'Map cells to reference'

Check it out, run a demo, and map your own datasets: https://t.co/6Cvnej2zaP