Biostar

695 results • Page 1 of 14

col_character(), CLIN_SIG = col_character(), SOMATIC = col_character(), PUBMED = col_logical(), TRANSCRIPTION_FACTORS = col_logical(), MOTIF_NAME = col_logical(), MOTIF_POS = col_logical(), HIGH_INF_POS

TCGA GDCprepare

updated 11 days ago • glaciya2018

Is there a way to fetch publications with redirected PMIDs? If so, how? For instance, the PMID 30134295 redirects to 30379686: https://pubmed.ncbi.nlm.nih.gov/30134295/ When I attempt to fetch the publication using the PMID 30134295, I get an error. I can manually check PubMed to see which PMID it redirects to, but I was wondering if there is a way to do it with Biopython. Thanks for any help…

pubmed pmid

updated 12 days ago • dominickd

database, reveals cell type-specific gene networks in the immune system” Paper in [PNAS][1] or [PubMed][2] Updates and other information will also be announced on twitter [@ImmunoNavigator][3]. Introduction ------------ The Immuno-Navigator...sites. [1]: http://www.pnas.org/content/113/17/E2393.short [2]: https://www.ncbi.nlm.nih.gov/pubmed/27078110 [3]: https://twitter.com/ImmunoNaviga…

gene-co-expression batch-effect immunology

updated 17 days ago • alexis.vandenbon

to a bioinformatics application. Yes, I have some applications that I have found through Google and PubMed but I'd like to see if others know about anything that I missed. Thanks

genAI chatgpt

updated 4 weeks ago • a615ebfb

interaction_info["QUANTITATION"], "Qualification": interaction_info["QUALIFICATIONS"], "Pubmed Author": interaction_info["PUBMED_AUTHOR"] } interactions.append(interaction_entry) # Convert to Pandas DataFrame

BioGRID Python REST

updated 5 weeks ago • dbykov

Suppose one is interested in a manuscript, and the RNA-Seq data it provides. So, she/he goes to BioProject, and picks up all the samples and metadata from SRA. Suppose in addition, one downloads the sample metadata as a part of (example) Supplemental Table S4 from the manuscript itself, then compares that to metadata housed in the correspondent Entrez DB records for those samples, with a view to…

NCBI Entrez SRA Journal Metadata

updated 10 weeks ago • LauferVA

DEFINITION, VERSION, DBSOURCE, KEYWORDS, and if possible publication information (A list of relevant pubmed entries for example would be amazing). A screenshot of such a file is shown here: https://www.genbeans.org/ibe/5.3/help

download peptide

updated 3 months ago • cs

Hi. Is there a way to get which terms matched each retrieved result? Here's an example of an API call: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term="yhiM" AND (metal OR Magnesium-cobalt OR Lead OR Magnesium) AND (resistan* OR toleran*) NOT (antibiotic* OR drug OR multidrug...s an example of an API call: https://eutils.ncbi.nlm.nih.gov/entrez/…

NCBI API

updated 3 months ago • langziv

receiving this output since 6:20 am UTC instead of the standard XML/JSON output when making calls to PubMed Eutils. URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=37716365&retmode=xml&amp

eutils pubmed

updated 5 months ago • rajvaghela23

Hello everyone, I have done a mesh search in pubmed for some certain keywords, I have got PMIDs for the result, Now I want to download all pdfs using those PMIDs in R. I have...rcrossref", "xml2")) library(rentrez) library(rcrossref) library(xml2) # Function to get DOI from PubMed ID get_doi <- function(pmid) { query <- entrez_fetch(db = "pubmed", id = pmid, rettype = "medline"…

R PubMed

updated 5 months ago • Confused_human

Tracking daily papers Tracking weekly papers Tracking review period in last 3 months from Pubmed Allow to add interesting papers into Reading list

paper

updated 6 months ago • charlin

www.embraceregistry.net/ [3]: http://www.biocatalogue.org/ [4]: http://www.ncbi.nlm.nih.gov/pubmed/16845108 [5]: http://www.ncbi.nlm.nih.gov/pubmed/18056132

web-service subjective

updated 6 months ago • Michael

that the latest paper shows up first (in reverse chronology). ## Let's obtain this information from PubMed ## The cleanFun cleans the html string and convert the string into dates cleanFun <- function(htmlString) { return(anytime

scholar easyPubMed

updated 6 months ago • rohitsatyam102

Is there a way to query pubmed articles that includes the type of data included? For instance, suppose I wanted to locate all pubmed articles where...data and genotype data (of some kind) are both provided. some of this can be done using the pubmed advanced search page, here: https://pubmed.ncbi.nlm.nih.gov/advanced/. But, I dont see a way to filter by data availability...to anther ncbi site, …

search data pubmed query

updated 6 months ago • LauferVA

A search in pubmed for chatGpt returns: - 0 articles in 2021 - 4 articles in 2022 - 1238 articles (as of Sept 17) in 2023 https://pubmed.ncbi.nlm.nih.gov

growth pubmed

updated 7 months ago • LauferVA

the print name for structure name. I use this e-link ```py record = Entrez.read(Entrez.elink(dbfrom="Pubmed", db="pccompound", ıd="6UFO")) print(record) ``` and it print as [{'LinkSetDbHistory': [], 'ERROR': [], 'LinkSetDb': [], 'DbFrom': 'Pubmed', 'IdList': ['6']}] but I would

pubchem elink entrez

updated 8 months ago • iamsmor

for taking the time to read this. I would like to know if it is possible to filter results from the PubMed API by e.g. article type (only show meta analysis/clinical trial/etc) or use the additional filters such as species My...code: import requests import json db = 'pubmed' domain = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils' query = "cancer" retmode='jso…

pubmed-api pubmed entrez esearch python

updated 9 months ago • kolja.o37

I would like to use a tool that will take any valid pubmed query, extract the abstracts, and create a [wordle][1] diagram. Ideally it would be a one-click operation that automatically

pubmed

updated 10 months ago • Andrew Su

RNA-seq data processing. Appl. Environ. Microbiol. In press. http://www.ncbi.nlm.nih.gov/pubmed/22798355

python rna-seq next-gen illumina

updated 10 months ago • cl.parallel

harbor Mendelian mutations. [1]: http://www.svaproject.org/ [2]: http://www.ncbi.nlm.nih.gov/pubmed/21624899

snp variant-annotation

updated 10 months ago • Malachi Griffith

can be found [here][3]. [1]: http://snpeff.sourceforge.net/ [2]: http://www.ncbi.nlm.nih.gov/pubmed/22728672 [3]: http://snpeff.sourceforge.net/faq.html#What_effects_are_predicted

snp variant-annotation

updated 10 months ago • Malachi Griffith

vat.gersteinlab.org [1]: http://vat.gersteinlab.org/index.php [2]: http://www.ncbi.nlm.nih.gov/pubmed/22743228

snp variant-annotation

updated 10 months ago • Malachi Griffith

1]: http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do [2]: http://www.ncbi.nlm.nih.gov/pubmed/22618869

snp variant-annotation

updated 10 months ago • Malachi Griffith

literature from public databases using proprietary text-mining algorithms. BioGyan fetches PubMed abstracts, biological pathways and 3D-structures of proteins based on user specified search terms. BioGyan has the...following features: - Facilitates combinatorial search using databases like PubMed, NCBI Gene, UniProt, PDB, etc. - Allows offline reading of abstracts - Ranks abstracts based on …

gene pubmed software

updated 10 months ago • reachtoskumar

Until LinkedIn allows us to import our publications directly from ResearchGate, Google Scholar, Pubmed,... the LinkedIn's publications' section can be populated by searching by PubMed ID or by DOI though this GreaseMonkey...script: [LinkedIn PubMed Importer v1.4][1] [1]: http://alternateallele.com/alternatealle/2015/5/4/linkedin-pubmed-importer-v14

GreaseMonkey LinkedIn PubMed DOI

updated 10 months ago • Jorge Amigo

5]'. The tool takes sequence reads in a variety of formats. [1]: http://view.ncbi.nlm.nih.gov/pubmed/22307239 [2]: http://liulab.dfci.harvard.edu/MACS/ [3]: http://massgenomics.org/2010/12/uniqueness-mappability-human-genome.html

chip-seq

updated 10 months ago • Ian

Brief Bioinform. 2017 Jan 17. pii: bbw143. doi: 10.1093/bib/bbw143. https://www.ncbi.nlm.nih.gov/pubmed/28096075 Please let me know if you encounter any issues when using this pipeline. (email address: wangdp123@gmail.com

sequence R genome snp RNA-Seq

updated 10 months ago • wangdp123

enter image description here][1] The image is taken from: https://www.ncbi.nlm.nih.gov/pubmed/26773003 [1]: http://ivanya.com/tmp/2016/1024.tree.png

tree

updated 10 months ago • ivan.antonov

Gene Prioritization for Precision Oncology*. Genome Research. [doi:10.1101/gr.221218.117][5] ([PubMed: 28768687][6]) - Shrestha et al. (2014) *HIT’nDRIVE: Multi-driver gene prioritization based on hitting time*. In Sharan R, editor...5]: http://dx.doi.org/10.1101/gr.221218.117 [6]: https://www.ncbi.nlm.nih.gov/pubmed/28768687 [7]: https://link.springer.com/chapter/10.1007/978-3-319-05269…

network driver-gene software

updated 10 months ago • raunakms

Hello everyone, I developed a bioinformatics tool to visualize human genome pathways. [http://www.iprotein.info][1] When I was doing molecular biology research myself, I always had difficulty to get an overview of some genes in the vast human genome network. We often search it through Google image for pathways maps, or search from antibody companies, but these sources of pathways maps are hard…

reactome signalling visualization pathway

updated 10 months ago • serena_yu

We have released [LINK][1] (LIterature coNcept Knowledgebase), the latest resource in our Open Targets toolkit. `LINK` is a free resource that allows you to explore more than 500 million relations between genes, diseases, drugs and other key concepts. We have used [natural-language processing][2] (NLP) to extract these connections from PubMed abstracts. `LINK` is more than just a repository of…

NLP drug disease gene Open-Targets

updated 10 months ago • Denise CS

wwcrc/cnv_facets [2]: https://github.com/mskcc/facets [3]: https://www.ncbi.nlm.nih.gov/pubmed/27270079 [4]: https://i.imgur.com/l0Ru50L.png [5]: https://imgur.com/l0Ru50L

CNV somatic facets cancer

updated 10 months ago • dariober

This is what I have done: esearch -db pubmed -query "lycopene cyclase" | efetch -format abstract I was struck by this error: ``` 500 Can't connect to eutils.be-md.ncbi.nlm.nih.gov...No do_post output returned from 'https://eutils.be-md.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&query_key=1&WebEnv=NCID_1_67454450_130.14.18.34_9001_1529992046_810451412_0MetA0_S_Mega…

edirect pubmed NCBI

updated 10 months ago • zorn21g

of splicing and what the maximum and minimum values are? I read https://www.ncbi.nlm.nih.gov/pubmed/15285897, but it isn't quite clear to me yet

splice-scores MaxEntScan

updated 10 months ago • ga87mit

Hi, Is any tool/method to convert article title to pubmed ID? Anyone know? Thank you

pubmed

updated 10 months ago • BIOTIN

doi.org/10.11418/jtca1981.18.4_329) and two versions of the Masters (https://www.ncbi.nlm.nih.gov/pubmed/11416159) algorithm. - You can define search modes: deciding if amelogenin is taken into account or not and how the program

STR-profile Cell-line

updated 10 months ago • Amos Bairoch

M. 2016. GenVisR: Genomic Visualizations in R. Bioinformatics. pii: btw325. [Epub ahead of print] [PubMed][1] | [Bioinformatics Journal][2] | [BioRxiv][3] | [Bioconductor][4] | [GitHub][5] The following functions are available: - lolliplot - Visualize...www.biostars.org/p/196576/ ![GenVisR sample figures][6] [1]: http://www.ncbi.nlm.nih.gov/pubmed/27288499 [2]: https://doi.org/10.1093/…

visualization genomic RNA-Seq genvisr

updated 10 months ago • Obi Griffith

Divide citations and RCR metrics by the number of the authors. The metrics are calculated based on PUBMED (17M publications) and ORCID (600k profiles). More in bioRXiv preprint: https://lnkd.in/gMjTsh5 ---------- Number of authors vs research_non

PUBMED ORCID scientometrics bibliometrics

updated 10 months ago • Lukasz Kozlowski

Searching on PubMed but Internet speed is too bad? - File opening failed again! Published papers are too many to check and they cannot - I don...installation is successful: - Usage: pypubmed [OPTIONS] COMMAND [ARGS]... - Toolkits for NCBI Pubmed View the current version: pypubmed --version Update pypubmed to the latest version: pip3 install -U pypubmed **3. Add API_KEY...1. K…

python pubmed software

updated 10 months ago • Novogene

and I'd like to perform an enrichment analysis in order to get GO terms, KEGG pathways and, possibly, PubMed IDs statistically overrepresented. I performed some analysis using DAVID. Unfortunately I noticed that DAVID is

gene-set-enrichment-analysis

updated 10 months ago • ncl.lazzarini

bcftools ensembl-vep vep

updated 10 months ago • amy__

the use of sentiment analysis on the title and abstract fields of research articles indexed by Pubmed? I ran some more generic SA tools, but sanity checking of the results produced appeared to identify a skew towards calling

sentiment-analysis pubmed Python R

updated 10 months ago • LauferVA

conservation scores per base and identifying blocks of conserved regions within genes. 2. PIECE (pubmed 21041978) and SVC (pubmed 15991338) for exon-intron comparisons. 3. Synmap for whole genome synteny. 4. Gevo to visualize

evolution

updated 10 months ago • hbw

Tree #1 from https://www.ncbi.nlm.nih.gov/pubmed/26773003 : ![enter image description here][1] Tree #2 from http://www.fisht1k.org/subproject/phylogeny : ![enter image description

phylogenetic-tree

updated 10 months ago • ivan.antonov

on information extraction from biomedical text. So, I have come across many useful databases like PubMed, UniProt etc. But the biggest issue is that every source provides the data in xml format along with corresponding XSD

PubMed Database

updated 10 months ago • ashimgupta95

of biomedical and genomic information, and scientists all over the world use its products, including PubMed, ClinicalTrials.gov, GenBank, RefSeq, and ClinVar. Required Skills - 5+ years of experience running operations in a large

ClinVar

updated 10 months ago • jyu

civic

updated 10 months ago • bt_cepo

portal is the alma mater for biomedical research data. NCBI hosts the popular data resources like PubMed, PubChem, GenBank, RefSeq, GEO, SRA and dozens of other important Biomedical Data resources that are in the forefront...Expression Omnibus - Sequence Read Archive - ClinVar - dbSNP - Conserved Domain Database - Taxonomy - PubMed - PubChem - Retrieving Reference Genomes and Sequences - BLAST to…

Resources NCBI Biomedical Researchers Programming

updated 11 months ago • AABI

jayajit-das. Recent publications from the group can be found at, https://www.ncbi.nlm.nih.gov/pubmed/?term=jayajit+das . Das lab has access to a state of the art computer cluster over 120 INTEL processors. Resources at the

assembly

updated 11 months ago • jayajit

CPM`? Are these two different scale factors? Thanks [1]: https://www.ncbi.nlm.nih.gov/pubmed/30361341

Deeptools ATAC-seq

updated 11 months ago • Zeel

695 results • Page 1 of 14

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