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  • 2020-2024
  • Research software

  • Authors: Tremmel, Roman; Zhou, Yitian; Lauschke, Volker;

    A repository and search tool for worldwide country-specific pharmacogenetic allele frequencies Polymorphisms in drug metabolizing enzymes, drug transporters, and major histocompatibility complex genes cause significant inter-individual differences in drug efficacy and safety. The pattern and complexity of these variations differ across populations. PharmFreq is a global repository of pharmacogenetic frequency data from over 10 million individuals across hundreds of countries, aggregating data on pharmacogenomic alleles from over 1200 studies. The majority of studies focus on East Asian and European populations. The number of studies per country correlates with population size and GDP, with significant coverage disparities. All data is accessible via an interactive web dashboard at pharmfreq.com, providing a comprehensive resource for exploring pharmacogenetic diversity and guiding research in underrepresented populations. Note This repository contains a lightweight version of the code and database files used in our publication. For access to the most recent version of the database and the full web application, please visit www.pharmfreq.com. What's Included Code: A streamlined version of the shiny app. Inital database files.For detailed documentation and updates and most recent version of the database, refer to the main website linked above. Please cite the following paper if you use the data, website, or code. The resource is published and can be accessed here: PharmFreq: a comprehensive atlas of ethnogeographic allelic variation in clinically important pharmacogenesDOI: 10.1093/nar/gkae1016.

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  • Authors: Pestilli, Franco; Sani, Ilaria;

    Quantitative properties and tract profiles of the connections linking three key attentional control nodes located in the frontal, parietal and temporal lobes

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    Authors: Klenzing, Jeff; Stoneback, Russell; Burrell, Angeline G.; Smith, Jonathon; +2 Authors

    The v0.0.4 release adds improved xarray support, as well as JPL GPS data. Changes Update instrument tests with new test class Support xarray datasets through cdflib Preferentially loads data into pandas using pysatCDF if installed Adds pysatCDF to optional requirements invoked via '[all]' option at installation New Instruments JPL GPS ROTI Bug Fixes Fixed a bug in metadata when loading GOLD Nmax data. Fixed a bug in user feedback for methods.cdaweb.download Fixed a bug in loading ICON IVM data (added multi_file_day = True) Allow for array-like OMNI HRO meta data Fixed date handling for OMNI HRO downloads Updated filenames for TIMED SABER Maintenance Reduce duplication of code in instrument modules Include flake8 linting of docstrings and style in Github Actions Move OMNI HRO custom functions to a methods module Deprecate OMNI HRO custom functions in instrument module Update GitHub actions to the latest versions Added downstream test to test code with pysat RC Remove deprecated convert_timestamp_to_datetime calls Remove deprecated pandas syntax Added version cap for xarray 2022.11 Documentation New logo added

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    This code release accompanies Gasperi et al, Communications Biology 2021

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    These are the weights required to run the brain extraction tool provided at https://github.com/CAAI/HD-CTBET. The repo is a fork of the original model for MRI-based BET: https://github.com/MIC-DKFZ/hd-bet

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    Authors: Chris German; Seyoon Ko; Benjamin Chu; Hua Zhou;

    MendelPlots v0.1.6 Diff since v0.1.5 Merged pull requests: make manhattan annotations appear before circled dots (#3) (@biona001) compat update (#10) (@kose-y)

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    Authors: Harshil Patel; Phil Ewels; Alexander Peltzer; Olga Botvinnik; +26 Authors

    What's Changed Display a warning when '--extra_star_align_args' are used with RSEM by @MatthiasZepper in https://github.com/nf-core/rnaseq/pull/1049 Update public_aws_ecr.config by @maxulysse in https://github.com/nf-core/rnaseq/pull/1048 Remove public_aws_ecr profile by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1051 Important! Template update for nf-core/tools v2.9 by @nf-core-bot in https://github.com/nf-core/rnaseq/pull/1053 Update credits for subway map by @maxulysse in https://github.com/nf-core/rnaseq/pull/1057 Use nf-validation plugin for parameter and samplesheet validation by @drpatelh in https://github.com/nf-core/rnaseq/pull/1058 fix copy paste typo by @hmehlan in https://github.com/nf-core/rnaseq/pull/1062 Update untar by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1068 README.md: Added ref to downstream analyses by @smoe in https://github.com/nf-core/rnaseq/pull/1060 Update the CODE_OF_CONDUCT and CONTRIBUTING with nf-core template 2.10 by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1088 Reorganise arguments for clearer syntax by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1091 Reorganise local modules into subfolder/main.nf for consistency by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1083 Important! Template update for nf-core/tools v2.10 by @nf-core-bot in https://github.com/nf-core/rnaseq/pull/1078 Update usage.md for igenomes warning by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1073 Update all nf-core/modules in pipeline by @drpatelh in https://github.com/nf-core/rnaseq/pull/1093 update config to enable usage of a custom config by @maxulysse in https://github.com/nf-core/rnaseq/pull/1108 Kallisto quantification by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1106 Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1107 Pre-release fixes for 3.13.0 by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1114 Maxime feedback by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1116 FIX: Subway map by @maxulysse in https://github.com/nf-core/rnaseq/pull/1117 final updates on subway map by @maxulysse in https://github.com/nf-core/rnaseq/pull/1120 Dev -> Master for 3.13.0 release by @drpatelh in https://github.com/nf-core/rnaseq/pull/1113 New Contributors @hmehlan made their first contribution in https://github.com/nf-core/rnaseq/pull/1062 @pinin4fjords made their first contribution in https://github.com/nf-core/rnaseq/pull/1068 @smoe made their first contribution in https://github.com/nf-core/rnaseq/pull/1060 Full Changelog: https://github.com/nf-core/rnaseq/compare/3.12.0...3.13.0

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    Authors: Paschalis Chatzopoulos; Bob Muscarella;

    This is the first release of our repository.

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    This is the first release.

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201,553 Research products
  • Authors: Tremmel, Roman; Zhou, Yitian; Lauschke, Volker;

    A repository and search tool for worldwide country-specific pharmacogenetic allele frequencies Polymorphisms in drug metabolizing enzymes, drug transporters, and major histocompatibility complex genes cause significant inter-individual differences in drug efficacy and safety. The pattern and complexity of these variations differ across populations. PharmFreq is a global repository of pharmacogenetic frequency data from over 10 million individuals across hundreds of countries, aggregating data on pharmacogenomic alleles from over 1200 studies. The majority of studies focus on East Asian and European populations. The number of studies per country correlates with population size and GDP, with significant coverage disparities. All data is accessible via an interactive web dashboard at pharmfreq.com, providing a comprehensive resource for exploring pharmacogenetic diversity and guiding research in underrepresented populations. Note This repository contains a lightweight version of the code and database files used in our publication. For access to the most recent version of the database and the full web application, please visit www.pharmfreq.com. What's Included Code: A streamlined version of the shiny app. Inital database files.For detailed documentation and updates and most recent version of the database, refer to the main website linked above. Please cite the following paper if you use the data, website, or code. The resource is published and can be accessed here: PharmFreq: a comprehensive atlas of ethnogeographic allelic variation in clinically important pharmacogenesDOI: 10.1093/nar/gkae1016.

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  • Authors: Pestilli, Franco; Sani, Ilaria;

    Quantitative properties and tract profiles of the connections linking three key attentional control nodes located in the frontal, parietal and temporal lobes

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    Authors: Klenzing, Jeff; Stoneback, Russell; Burrell, Angeline G.; Smith, Jonathon; +2 Authors

    The v0.0.4 release adds improved xarray support, as well as JPL GPS data. Changes Update instrument tests with new test class Support xarray datasets through cdflib Preferentially loads data into pandas using pysatCDF if installed Adds pysatCDF to optional requirements invoked via '[all]' option at installation New Instruments JPL GPS ROTI Bug Fixes Fixed a bug in metadata when loading GOLD Nmax data. Fixed a bug in user feedback for methods.cdaweb.download Fixed a bug in loading ICON IVM data (added multi_file_day = True) Allow for array-like OMNI HRO meta data Fixed date handling for OMNI HRO downloads Updated filenames for TIMED SABER Maintenance Reduce duplication of code in instrument modules Include flake8 linting of docstrings and style in Github Actions Move OMNI HRO custom functions to a methods module Deprecate OMNI HRO custom functions in instrument module Update GitHub actions to the latest versions Added downstream test to test code with pysat RC Remove deprecated convert_timestamp_to_datetime calls Remove deprecated pandas syntax Added version cap for xarray 2022.11 Documentation New logo added

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    This code release accompanies Gasperi et al, Communications Biology 2021

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    These are the weights required to run the brain extraction tool provided at https://github.com/CAAI/HD-CTBET. The repo is a fork of the original model for MRI-based BET: https://github.com/MIC-DKFZ/hd-bet

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    Authors: Chris German; Seyoon Ko; Benjamin Chu; Hua Zhou;

    MendelPlots v0.1.6 Diff since v0.1.5 Merged pull requests: make manhattan annotations appear before circled dots (#3) (@biona001) compat update (#10) (@kose-y)

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