@shefflab
Joined May 2017
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  • Following27
  • Followers43
Taming the reference genome jungle: the refget sequence collection standard biorxiv.org/content/10.1101/… #biorxiv_genomic

Taming the reference genome jungle: the refget sequence collection standard

Reference genomes are foundational to genomics but suffer from widespread ambiguity and incompatibility due to inconsistent naming, undocumented differences, and lack of formal mechanisms for...

biorxiv.org
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BEDMS: A metadata standardizer for genomic regionattributes biorxiv.org/cgi/content/shor… #biorxiv_genomic
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Refget: standardised access to reference sequences biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Identity and compatibility of reference genome resources biorxiv.org/cgi/content/shor… #biorxiv_genomic
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Ref genie is some pretty slick work from @shefflab. If you don’t know, now you know.
S. Carson Callahan@scarsoncallahan
18 Nov 2020
Replying to @tangming2005
My lazy approach has been to use refgenie when possible: academic.oup.com/gigascience… It's pretty easy to pull things and if someone asks which versions of files you used, you just link the repo.

Refgenie: a reference genome resource manager

AbstractBackground. Reference genome assemblies are essential for high-throughput sequencing analysis projects. Typically, genome assemblies are stored on

academic.oup.com
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Bedshift: perturbation of genomic interval sets biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Great example of multiple awesome #communities working well #together. Honored to have been able to contribute. #usegalaxy #refgenie #cvmfs #referencedata #opendata
Michał Stolarczyk@m_stolarczyk
12 Oct 2020
Refgenie assets can be the source of reference datasets in Galaxy @galaxyproject Happy to share the preprint on the integration of refgenie into the Galaxy platform: biorxiv.org/content/10.1101/…

Expanding the Galaxy’s reference data

Summary Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows to easily organize,...

biorxiv.org
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PEPATAC: An optimized ATAC-seq pipeline with serial alignments biorxiv.org/cgi/content/shor… #biorxiv_genomic
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Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects biorxiv.org/content/10.1101/… Code: github.com/pepkit docs: pep.databio.org/en/latest/. Really useful stuff out of @shefflab
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Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Want to annotate sources of epigenetic variation in your DNA methylation, ATAC-seq, or multi-omics data? Check out the paper on our Bioconductor package, now out in Genome Biology. @shefflab @UVABME @uva_biodatasci @Bioconductor
Genome Biology@GenomeBiology
11 Sep 2020
COCOA: coordinate covariation analysis for epigenetic heterogeneity, from @OmicDataScience, Sheffield and co. Analyzes covariation of epigenetic data across individuals eg can predict ER status of breast cancer from methylation. Also can use ATAC-seq etc genomebiology.biomedcentral.…
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Analytical Approaches for ATAC-seq Data Analysis. dlvr.it/RYpCy7
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Nathan Sheffield retweeted
Michael Love@mikelove
21 Jul 2020
This looks super useful for compiling various overlaps for genomic regions
Levi Waldron@LeviWaldron1
21 Jul 2020
Replying to @LeviWaldron1
GenomicDistributions: a new Bioconductor-oriented package that calculates and plots genomic data. f1000research.com/posters/9-…
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Nathan Sheffield retweeted
bioRxiv@biorxivpreprint
11 Jul 2020
COCOA: Coordinate covariation analysis of epigenetic heterogeneity biorxiv.org/content/10.1101/… #bioRxiv
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IGD: high-performance search for large-scale genomic interval datasets biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Quality control and processing of nascent RNA profiling data biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Happy to share our @GigaScience paper introducing Refgenie. Make sure to check out the tool, especially if you regularly use reference genome-related data! @shefflab doi.org/10.1093/gigascience/… - refgenie docs: refgenie.databio.org - refgenomes server: refgenomes.databio.org/
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Refgenie: a reference genome resource manager biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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