Hammer Lab
@hammer_lab
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We're a lab working to understand and improve the immune response to cancer at @muschollings
Charleston, SC
Joined June 2014
Our lab member Eric Czech will present this work at #biodata18 on Saturday. The source code is available at https://t.co/9cEHh1GSLy. If you're interested in GPU-accelerated open source software for the analysis of multiplex tissue imaging data, we'd appreciate your feedback!
github.com
Microscopy Image Cytometry Toolkit. Contribute to hammerlab/cytokit development by creating an account on GitHub.
Cytokit: A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging https://t.co/0OEIlEwhHq
#bioRxiv
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This is what we have been working on at @hammer_lab for the last few months: Human Primary T Cells: A Practical Guide - Live document: https://t.co/CUaGiSVE3g - Code/data: https://t.co/xYqMYyKuZ6 - Protocols: https://t.co/6rm6W4q4mw cc: @PINPINPINN @Chrystal_Paulos
protocols.io
Human primary T cells are invaluable and feasible model systems to study the characteristics of the human immune cells in various contexts, including but not limited to cancer i...
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A few of our former lab members have formed a new lab to continue their work on open source software for neoantigen vaccines. Go follow them at @OpenVax!
It's still a work in progress, but I just made a website for the new @openvax lab at Mount Sinai: https://t.co/S462kKP6xq. Focus: machine learning applied to immunology, neoantigens, personalized cancer vaccines.
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New preprint! Prohlatype: A Probabilistic Framework for HLA Typing by @leonidrozenberg
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We just released MHCflurry 1.0, our MHC I ligand prediction package. 20% more alleles, over 10X faster, docs, and an accuracy boost. Happy predicting! https://t.co/TqsdL4Lcri
@hammer_lab
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Introducing spark-bam, a foundational library that enables the distributed processing of aligned reads with @ApacheSpark, by @RunsAsCoded:
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New preprint from @smondet on how our lab uses @OCamlLang to manage complex bioinformatics workflows on cloud, Hadoop, and HPC environments
Bioinformatics Workflow Management With The Wobidisco Ecosystem https://t.co/v2vx4G1L9Q
#biorxiv_bioinfo
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We've posted a preprint that describes the open source software powering the neoantigen vaccine trial described at https://t.co/myjNDkitSH
New preprint: "Computational pipeline for the PGV-001 neoantigen vaccine trial".
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@timodonnell File issues and contribute code at
github.com
Peptide-MHC I binding affinity prediction. Contribute to openvax/mhcflurry development by creating an account on GitHub.
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@timodonnell Read the preprint, "MHCflurry: open-source class I MHC binding affinity prediction”, at
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Introducing SurvivalStan, with an epic introduction to Bayesian survival analysis with @mcmc_stan, by @jackiburos:
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A broad but shallow review of informatics in cancer immunotherapy:
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@RunsAsCoded @ApacheSpark @googlecloud You can too with Pageant, our Apache-licensed Parallel Genomic Analysis Toolkit:
github.com
Parallel Genomic Analysis Toolkit. Contribute to hammerlab/pageant development by creating an account on GitHub.
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Watch: @RunsAsCoded shows how our lab uses @ApacheSpark on @googlecloud to process thousands of BAMs in a few hours
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For the Apache 2.0-licensed Vaxrank code, check out
github.com
Ranked vaccine peptides for personalized cancer immunotherapy - openvax/vaxrank
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We use Vaxrank in our clinical trial that’s actively recruiting patients; for more on the trial see
opentrials.net
All the Data, on All the Trials, Linked
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New preprint! Vaxrank: A Computational Tool For Designing Personalized Cancer Vaccines
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We’re quite proud of this paper! One reviewer: “It sets the bar for ... biomarker analyses in patients treated with checkpoint inhibitors”
Tumor and immune features associated w/ clinical response to checkpioint blockade therapy in urothelial #Cancer
https://t.co/RwEIM7voPw
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