Comprehensive and scalable quantification of splicing differences with MntJULiP
Abstract Tools for differential splicing detection have failed to provide a comprehensive and consistent view of splicing variation. We present MntJULiP, a novel method for comprehensive and accurate quantification of splicing differences between two or more conditions. MntJULiP detects both changes...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-09-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-022-02767-y |
| _version_ | 1811267495513817088 |
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| author | Guangyu Yang Sarven Sabunciyan Liliana Florea |
| author_facet | Guangyu Yang Sarven Sabunciyan Liliana Florea |
| author_sort | Guangyu Yang |
| collection | DOAJ |
| description | Abstract Tools for differential splicing detection have failed to provide a comprehensive and consistent view of splicing variation. We present MntJULiP, a novel method for comprehensive and accurate quantification of splicing differences between two or more conditions. MntJULiP detects both changes in intron splicing ratios and changes in absolute splicing levels with high accuracy, and can find classes of variation overlooked by other tools. MntJULiP identifies over 29,000 differentially spliced introns in 1398 GTEx brain samples, including 11,242 novel introns discovered in this dataset. Highly scalable, MntJULiP can process thousands of samples within hours to reveal splicing constituents of phenotypic differentiation. |
| first_indexed | 2024-04-12T21:04:42Z |
| format | Article |
| id | doaj.art-4f20c300f9d94008974eaa0194b61e20 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-04-12T21:04:42Z |
| publishDate | 2022-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-4f20c300f9d94008974eaa0194b61e202022-12-22T03:16:45ZengBMCGenome Biology1474-760X2022-09-0123111610.1186/s13059-022-02767-yComprehensive and scalable quantification of splicing differences with MntJULiPGuangyu Yang0Sarven Sabunciyan1Liliana Florea2Department of Computer Science, Johns Hopkins UniversityDepartment of Pediatrics, Johns Hopkins School of MedicineMcKusick-Nathans Department of Genetic Medicine, Johns Hopkins School of MedicineAbstract Tools for differential splicing detection have failed to provide a comprehensive and consistent view of splicing variation. We present MntJULiP, a novel method for comprehensive and accurate quantification of splicing differences between two or more conditions. MntJULiP detects both changes in intron splicing ratios and changes in absolute splicing levels with high accuracy, and can find classes of variation overlooked by other tools. MntJULiP identifies over 29,000 differentially spliced introns in 1398 GTEx brain samples, including 11,242 novel introns discovered in this dataset. Highly scalable, MntJULiP can process thousands of samples within hours to reveal splicing constituents of phenotypic differentiation.https://doi.org/10.1186/s13059-022-02767-yAlternative splicingDifferential splicingTranscriptomicsRNA-seq |
| spellingShingle | Guangyu Yang Sarven Sabunciyan Liliana Florea Comprehensive and scalable quantification of splicing differences with MntJULiP Genome Biology Alternative splicing Differential splicing Transcriptomics RNA-seq |
| title | Comprehensive and scalable quantification of splicing differences with MntJULiP |
| title_full | Comprehensive and scalable quantification of splicing differences with MntJULiP |
| title_fullStr | Comprehensive and scalable quantification of splicing differences with MntJULiP |
| title_full_unstemmed | Comprehensive and scalable quantification of splicing differences with MntJULiP |
| title_short | Comprehensive and scalable quantification of splicing differences with MntJULiP |
| title_sort | comprehensive and scalable quantification of splicing differences with mntjulip |
| topic | Alternative splicing Differential splicing Transcriptomics RNA-seq |
| url | https://doi.org/10.1186/s13059-022-02767-y |
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