Search Results for "pubmed"
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Showing 54 open source projects for "pubmed"
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JabRef Bibliography Management
Graphical Java application for managing BibTeX and biblatex
JabRef is an open-source, cross-platform citation and reference management tool. Stay on top of your literature: JabRef helps you to collect and organize sources, find the paper you need and discover the latest research. JabRef is available free of charge and is actively developed. It supports you in every step of your research work. -
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PaperAI
Semantic search and workflows for medical/scientific papers
PaperAI is an open-source framework for searching and analyzing scientific papers, particularly useful for researchers looking to extract insights from large-scale document collections. -
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MLDatasets.jl
Utility package for accessing common Machine Learning datasets
This package represents a community effort to provide a common interface for accessing common Machine Learning (ML) datasets. In contrast to other data-related Julia packages, the focus of MLDatasets.jl is specifically on downloading, unpacking, and accessing benchmark datasets. Functionality for the purpose of data processing or visualization is only provided to a degree that is special to some datasets. -
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GROBID
A machine learning software for extracting information
...The extraction here covers the usual bibliographical information (e.g. title, abstract, authors, affiliations, keywords, etc.). References extraction and parsing from articles in PDF format, around .87 F1-score against on an independent PubMed Central set of 1943 PDF containing 90,125 references, and around .89 on a similar bioRxiv set of 2000 PDF (using the Deep Learning citation model). All the usual publication metadata are covered (including DOI, PMID, etc.). -
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Crossref Author Check
Web app to cross-check publication/authorship against CrossRef
This tool retrieves CrossRef information on article type, authorship, print date, subject area, etc. for publications specified by DOI and/or PubMed IDs (max. 100). The tool also tallies the order of authorship for a specified author. -
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ResearchWheel
Research the web without constantly switching tabs.
...With middle click open a wheel with many available actions: 🎓 North | Google Scholar - Search selected text or the webpage title 🧬 North-East |PubMed - Search selected text or the webpage title 📝 East | Append Note - Save selected text to the workspace 📚 South-East |Citation - Generate and copy a citation 📂 South | Workspace - Open the research sidebar 🌐 South-West |Translate - Translate webpage content 🔗 West | Title + URL - Copy a clean Markdown link 📋 North-West | Quote + Source - Copy selected text with source attribution -
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SimThyr
A simulation program for thyroid homeostasis.
SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients. -
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Gemi
PCR primers / probes design from multiple & degenerate sequences
...Milestone: The tool reached about 3000 downloads sine 2012. Article Gemi: PCR primers prediction from multiple alignments. Comparative and functional genomics 2012 PMID: https://www.ncbi.nlm.nih.gov/pubmed/23316117 A great review on designing primer, Gemi, and other tools: Designing degenerate primers: Overview, challenges, and computational methods. Methods in Microbiology. Vol 57, 2025, Pages 73-89; DOI: 10.1016/bs.mim.2025.01.002 -
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GENET-CNV
Integrated DNA copy number variation and gene expression analysis
...Ye Q, Singh S, Qian PR, Guo NL. Immune-Omics Networks of CD27, PD1, and PDL1 in Non-Small Cell Lung Cancer. Cancers. 2021;13(17). Epub 2021/09/11. doi: 10.3390/cancers13174296. PubMed PMID: 34503105. -
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Web based cataloging and dedupe application. Highly optimized for processing journal articles. Reads MarcXML and dedupes records using the field 773 combined with a fuzzy search on the title. Written for bibnet.org
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
... * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data using GSA-SNP2", Nucleic Acids Research, Vol. 46(10), e60(2018). * PubMed ID: 29562348 * DOI: 10.1093/nar/gky175 -> PLEASE MOVE OR MAKE A COPY OF 'DATA' FOLDER INTO YOUR INTENSIVE TEST FOLDER (I.E. LINUX, MAC OR WINDOWS SPECIFIED FOLDER) TO ALLOW THE PROGRAM TO FIND THE PREDESIGNED DATA. * UPDATE NOTE: -> Sep-1-2020: add an update for Ubuntu-20.04. You will need Boost library installed (sudo apt-get install libboost-all-dev) -> Mar-7-2018: revise header terms in the output file -
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A.I.G.Le is a French PHPMySQL code to simplify lab management. A.I.G.Le means "Aide Interactive a la Gestion de Laboratoire"
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Myelin water atlas
Normative myelin water atlas for myelin distribution in the brain
...The created myelin water atlas with its standard deviation can be used as a reference for your own studies related to myelin. A full description of this work can be found in this paper: https://www.ncbi.nlm.nih.gov/pubmed/31347238. -
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MWI spinal cord atlases
Normative atlases for the spinal cord using myelin water imaging
...These atlases (in PAM50 space from Spinal Cord toolbox) can be used as a reference to demonstrate areas of abnormalities in individuals with myelin-related disease and damage. A full description of this work can be found in this paper: https://www.ncbi.nlm.nih.gov/pubmed/31407400. -
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LOCUST
Custom Sequence Locus Typer
...Publication: Brinkac LM, Beck E, Inman J, Venepally P, Fouts DE, Sutton G. LOCUST: A Custom Sequence Locus Typer for Classifying Microbial Isolates. Bioinformatics (Oxford, England). 2017 Jan 27; https://www.ncbi.nlm.nih.gov/pubmed/28130240 -
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DualTranscriptDiscovery
Transcript-discovery approach for gene feature delimitation by RNA-seq
...A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model. Biology Open 7(1): bio028498. doi: 10.1242/bio.028498 PMID: 29183907. http://bio.biologists.org/content/7/1/bio028498 https://www.ncbi.nlm.nih.gov/pubmed/?term=29183907 -
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GNAT
GNAT recognizes gene names in text and maps them to NCBI Entrez Gene
GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/. -
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Pour la médecine fondée sur les faits (Evidence-Based Medicine (EBM)). La technique PICO pour formuler des questions cliniques. Plate-forme web open source pour supporter la création de PICO, la recherche et l'évaluation d'informations.
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Crosshub
Multi-way analysis of The Cancer Genome Atlas (TCGA) project datasets
...RNA-Seq vs. clinical (TNM, stage, follow-up) correlation analysis Generates Excel summaries. For details, see the manual or article G.S. Krasnov et al. NAR 2016, Pubmed ID: 26773058 -
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weinberg-overcluster2
Cluster subsequences of intergenic regions
...It clusters these subsequences based on the output of BLAST comparisons of the IGRs. overcluster2 has been used as part of a method to discover novel non-coding RNA classes. overcluster2 was written by Zasha Weinberg. The basic method was one of the methods described here: https://www.ncbi.nlm.nih.gov/pubmed/19340921 An example of the use of overcluster2 to find non-coding RNAs is here: https://www.ncbi.nlm.nih.gov/pubmed/20230605 -
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
...Minimal user defined parameters are required. Source code with user manual and installation guide of VFS is available at sourceforge's "Files" section. Citation: http://www.ncbi.nlm.nih.gov/pubmed/ -
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biogas_metagenome_binning
perl scripts to extract microbial genomes from metagenome assembly
...In this project we report a collection of perl scripts specifically designed for the binning procedure. Some of them were developed to perform in an automatic way the procedure proposed by Albertsen and coll. (http://www.ncbi.nlm.nih.gov/pubmed/?term=23707974), others are specifically developed for a newly developed binning strategy aimed to simplify the binning of hundreds of genomes and to estimate their completeness. -
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EDDA
Experiment Design for Differential Abundance Analysis
...“The Importance of Study Design for Detecting Differentially Abundant Features in High-Throughput Experiments.” Genome Biology 2014;15(12):527 (http://www.ncbi.nlm.nih.gov/pubmed/25517037/). An accompanying web server (http://edda.gis.a-star.edu.sg/) is available for easy access to some functionality of EDDA. Additionally a Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/EDDA.html) is available for easy installation of EDDA R package. -
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...Izaskun Mallona, Mireia Jordà, and Miguel A. Peinado. "A knowledgebase of the human Alu repetitive elements." Journal of biomedical informatics 60 (2016): 77-83. http://www.ncbi.nlm.nih.gov/pubmed/26827622
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CNVision
CNV prediction from Illumina genotyping data
...CNVision was written to analyze data for the Simons Simplex Collection (SSC) autism data. A fill description of methods are given in the following paper which can be used to reference CNVision: http://www.ncbi.nlm.nih.gov/pubmed/21658581
