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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Soelter, Tabea M.; Howton, Timothy C.; Clark, Amanda D.; Oza, Vishal H.; +1 Authors

    Data Release: The code and results accompany the "Altered Glia-Neuron Communication in Alzheimer's Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq" manuscript. Additionally, all data is publicly available on Zenodo including docker images, input files, processed files, and Seurat objects.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Software . 2023
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Software . 2023
    Data sources: ZENODO
    ZENODO
    Software . 2023
    License: CC BY
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Software . 2023
      License: CC BY
      Data sources: ZENODO
      ZENODO
      Software . 2023
      Data sources: ZENODO
      ZENODO
      Software . 2023
      License: CC BY
      Data sources: Datacite
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Fahad, Ahmed S.; Gutierrez-Gonzalez, Matias F.; Madan, Bharat; DeKosky, Brandon J.;

    This folder contains the scripts and example data associated with a publication led by Cold Spring Harbor Laboratory. "Quantitative analysis of functionally screened antibody repertoires for clonal identification and discovery" Ahmed S. Fahad1*, Matias F. Gutierrez-Gonzalez1*, Bharat Madan1, Brandon J. DeKosky1,2** 1-The Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA, USA 2-Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA *Equal contribution **Corresponding author. E-mail: dekosky@mit.edu Requirements: A UNIX-like enviroment. A computer cluster running on SLURM is ideal. IgBlast Fastx_toolkit FLASH usearch v5

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Software . 2023
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Software . 2023
    License: CC BY
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Software . 2023
      License: CC BY
      Data sources: ZENODO
      ZENODO
      Software . 2023
      License: CC BY
      Data sources: Datacite
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  • Authors: wang, xiaojing;

    Generate customized protein sequence database from RNA-Seq data for proteomics search.

    https://doi.org/10.1...arrow_drop_down
    bio.tools
    Software . 2017
    License: Artistic-2.0
    Data sources: bio.tools
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      https://doi.org/10.1...arrow_drop_down
      bio.tools
      Software . 2017
      License: Artistic-2.0
      Data sources: bio.tools
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Carifio, Jonathan; Gaibler, Volker; Norman, Henrik; Otor, O. Justin; +4 Authors

    pywwt is the official toolkit for accessing AAS WorldWide Telescope (WWT) from Python. Learn more at the pywwt website.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Software . 2022
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Software . 2022
    Data sources: ZENODO
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Software . 2022
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Software . 2022
      Data sources: ZENODO
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  • Authors: Stark, Sydney; Schall, Megan K.; Wagner, Tyler;

    Flathead Catfish _Pylodictis olivaris_ are a prominent aquatic invasive species within the United States and a recent invader in the Susquehanna River Basin, Pennsylvania. Flathead Catfish are piscivores known to consume native and recreationally important fish species. In the northeastern United States, it is unknown how this invader is impacting food webs and which species may be at greatest predation risk. To address this knowledge gap, we DNA barcoded stomach contents collected from Flathead Catfish to identify prey species and elucidate potential predatory impacts of Flathead Catfish in the Susquehanna River. A total of 576 Flathead Catfish were collected during 2020 – 2021, with 241 individuals having recoverable stomach contents. In all, we identified 47 different prey species. The most common prey species were rusty crayfish. While frequency of occurrence of prey species differed across Flathead Catfish length class. Rusty crayfish were commonly found (33.7 - 44.0% of diets) in stomachs of all size classes. We used a Bayesian hierarchical multivariate probit model to investigate if the probability of prey species occurrence in the diets of Flathead Catfish varied seasonally or as a function of Flathead Catfish length. We found that Flathead Catfish length and seasonality did influence prey occurrence probability differentially for a range of species. For example, Channel Catfish _Ictalurus punctatus_ were more likely to appear in shorter Flathead Catfish while Smallmouth Bass appeared in larger Flathead Catfish. We demonstrate significant variation in Flathead Catfish predatory effects that will be important to fisheries managers responsible for future management and monitoring strategies. This repository provides R scripts to analyze diet data for Flathead Catfish sampled in the Susquehanna River, PA.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/

    {"references": ["Deshpande et al. (2022) Network inference with Granger causality ensembles on single-cell transcriptomics. Cell Reports, 38:6."]} This release adds supplementary files associated with the manuscript.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Software . 2020
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Software . 2021
    Data sources: ZENODO
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Software . 2022
    Data sources: Datacite
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Software . 2022
    Data sources: ZENODO
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    downloaddownloads10
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Software . 2020
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Software . 2021
      Data sources: ZENODO
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Software . 2022
      Data sources: Datacite
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Software . 2022
      Data sources: ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Goto, Hiroki; Dickins, Benjamin; Afgan, Enis; Paul, Ian; +3 Authors

    Additional file 3: FN-FP-simulation-script.py. A script for performing simulation performed in Results and discussion. (PY 5 KB)

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    figshare
    Software . 2019
    License: CC BY
    Data sources: Datacite
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    figshare
    Software . 2019
    License: CC BY
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ figsharearrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      figshare
      Software . 2019
      License: CC BY
      Data sources: Datacite
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      figshare
      Software . 2019
      License: CC BY
      Data sources: Datacite
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  • The purpose of this software is to find sparse approximate solutions to linear equations. A classical method for this problem is L1-norm regularized least squares, but this often underestimates the amplitudes of the true solution values. As an alternative to the L1 norm, this software uses the generalized minimax-concave (GMC) penalty which maintains the convexity of the least squares cost function to be minimized. The GMC penalty is defined in terms of the generalized Huber function. The algorithm in this software minimizes the GMC sparse-regularized least squares cost function using a proximal algorithm comprising simple computations. This software is also available in MATLAB

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Team, Galaxy Support;

    Convert between various FASTQ quality formats for a list of inputs.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bio.toolsarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    bio.tools
    Software . 2016
    Data sources: bio.tools
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bio.toolsarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      bio.tools
      Software . 2016
      Data sources: bio.tools
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Sun, Sally; Ward, Owen G.; Wu, Jing; Xiao, Lihao; +2 Authors

    Temporal Point Processes are widely used to model phenomena in many fields, such as finance6and neuroscience. However, tools to evaluate the fit of these point processes to data, and to identify reasons for lack of fit, are not readily implemented in common software. Here weprovideppdiag, an R package containing a selection of statistically motivated tools to analyse9the goodness of fit of point processes to data, as have been described in Wu et al.(2020).

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Software . 2021
    Data sources: ZENODO
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    ZENODO
    Software . 2021
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      ZENODO
      Software . 2021
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2,308 Research products
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Soelter, Tabea M.; Howton, Timothy C.; Clark, Amanda D.; Oza, Vishal H.; +1 Authors

    Data Release: The code and results accompany the "Altered Glia-Neuron Communication in Alzheimer's Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq" manuscript. Additionally, all data is publicly available on Zenodo including docker images, input files, processed files, and Seurat objects.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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    ZENODO
    Software . 2023
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Software . 2023
    Data sources: ZENODO
    ZENODO
    Software . 2023
    License: CC BY
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Software . 2023
      License: CC BY
      Data sources: ZENODO
      ZENODO
      Software . 2023
      Data sources: ZENODO
      ZENODO
      Software . 2023
      License: CC BY
      Data sources: Datacite
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Fahad, Ahmed S.; Gutierrez-Gonzalez, Matias F.; Madan, Bharat; DeKosky, Brandon J.;

    This folder contains the scripts and example data associated with a publication led by Cold Spring Harbor Laboratory. "Quantitative analysis of functionally screened antibody repertoires for clonal identification and discovery" Ahmed S. Fahad1*, Matias F. Gutierrez-Gonzalez1*, Bharat Madan1, Brandon J. DeKosky1,2** 1-The Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA, USA 2-Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA *Equal contribution **Corresponding author. E-mail: dekosky@mit.edu Requirements: A UNIX-like enviroment. A computer cluster running on SLURM is ideal. IgBlast Fastx_toolkit FLASH usearch v5

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    ZENODO
    Software . 2023
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Software . 2023
    License: CC BY
    Data sources: Datacite
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      ZENODO
      Software . 2023
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      ZENODO
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  • Authors: wang, xiaojing;

    Generate customized protein sequence database from RNA-Seq data for proteomics search.

    https://doi.org/10.1...arrow_drop_down
    bio.tools
    Software . 2017
    License: Artistic-2.0
    Data sources: bio.tools
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      https://doi.org/10.1...arrow_drop_down
      bio.tools
      Software . 2017
      License: Artistic-2.0
      Data sources: bio.tools
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Carifio, Jonathan; Gaibler, Volker; Norman, Henrik; Otor, O. Justin; +4 Authors

    pywwt is the official toolkit for accessing AAS WorldWide Telescope (WWT) from Python. Learn more at the pywwt website.

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    ZENODO
    Software . 2022
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    ZENODO
    Software . 2022
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      ZENODO
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  • Authors: Stark, Sydney; Schall, Megan K.; Wagner, Tyler;

    Flathead Catfish _Pylodictis olivaris_ are a prominent aquatic invasive species within the United States and a recent invader in the Susquehanna River Basin, Pennsylvania. Flathead Catfish are piscivores known to consume native and recreationally important fish species. In the northeastern United States, it is unknown how this invader is impacting food webs and which species may be at greatest predation risk. To address this knowledge gap, we DNA barcoded stomach contents collected from Flathead Catfish to identify prey species and elucidate potential predatory impacts of Flathead Catfish in the Susquehanna River. A total of 576 Flathead Catfish were collected during 2020 – 2021, with 241 individuals having recoverable stomach contents. In all, we identified 47 different prey species. The most common prey species were rusty crayfish. While frequency of occurrence of prey species differed across Flathead Catfish length class. Rusty crayfish were commonly found (33.7 - 44.0% of diets) in stomachs of all size classes. We used a Bayesian hierarchical multivariate probit model to investigate if the probability of prey species occurrence in the diets of Flathead Catfish varied seasonally or as a function of Flathead Catfish length. We found that Flathead Catfish length and seasonality did influence prey occurrence probability differentially for a range of species. For example, Channel Catfish _Ictalurus punctatus_ were more likely to appear in shorter Flathead Catfish while Smallmouth Bass appeared in larger Flathead Catfish. We demonstrate significant variation in Flathead Catfish predatory effects that will be important to fisheries managers responsible for future management and monitoring strategies. This repository provides R scripts to analyze diet data for Flathead Catfish sampled in the Susquehanna River, PA.

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