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txdb.hsapiens.ncbi.hg38.mane

https://github.com/ctriermaansson/txdb.hsapiens.ncbi.hg38.mane

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
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    Academic publication links
    Links to: ncbi.nlm.nih.gov, nature.com
  • ○
    Committers with academic emails
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: CTrierMaansson
  • Language: R
  • Default Branch: main
  • Size: 9.91 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme Citation

README.md

Hits

TxDb.Hsapiens.NCBI.hg38.MANE

Description

A TxDb object to be used for genetic analysis in R. The object suited to be used as any TxDb object which can be explored with different Bioconductor packages, including GenomicFeatures. TxDb.Hsapiens.NCBI.hg38.MANE contains transcript information from the Matched Annotation from NCBI and EMBL-EBI (MANE) project which collects information from both the NCBI RefSeq and the EMBL-EBi Ensembl/GENCODE projects. The dataset contains information from representative protein coding transcripts and combines both transcript and gene identifiers.

Resources

The .gtf file used to create the package was downloaded from NCBI and was made into a TxDb object using txdbmaker.

The MANE project is described in Morales et al. 2022, Nature.

Installation

The package is installed directly from GitHub using devtools ```R if (!require(devtools)) install.packages('devtools') library(devtools)

devtools::installgithub("CTrierMaansson/TxDb.Hsapiens.NCBI.hg38.MANE") TxDbMANE <- TxDb.Hsapiens.NCBI.hg38.MANE::TxDb.Hsapiens.NCBI.hg38.MANE

```

Citation

Please site this package as Maansson, CT. (2024). TxDb.Hsapiens.NCBI.hg38.MANE (Version 1.0.0) [Computer software]. https://github.com/CTrierMaansson/TxDb.Hsapiens.NCBI.hg38.MANE

Owner

  • Name: Christoffer Trier Månsson
  • Login: CTrierMaansson
  • Kind: user
  • Location: Aarhus University Hospital

PhD student at AUH studying blood based biomarkers in lung cancer patients. My main focuses are epigenetic features in liquid biopsies and NGS.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Trier Maansson
    given-names: Christoffer
    orcid: https://orcid.org/0000-0002-3071-3437
title: "TxDb.Hsapiens.NCBI.hg38.MANE"
version: 1.0.0
date-released: 2024-06-07
url: https://github.com/CTrierMaansson/TxDb.Hsapiens.NCBI.hg38.MANE

GitHub Events

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  • Push event: 1
Last Year
  • Push event: 1

Committers

Last synced: 12 months ago

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  • Total Commits: 24
  • Total Committers: 1
  • Avg Commits per committer: 24.0
  • Development Distribution Score (DDS): 0.0
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  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
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Christoffer Trier Månsson 1****n 24

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Last synced: 12 months ago

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  • Bot issues: 0
  • Bot pull requests: 0
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Dependencies

DESCRIPTION cran
  • txdbmaker >= 1.0.0 depends
  • AnnotationDbi * imports