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paulstothard committed Jul 10, 2024
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- [nf-core/rnaseq](https://github.com/nf-core/rnaseq) - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
- [pachterlab/kallisto](https://github.com/pachterlab/kallisto) - Near-optimal RNA-Seq quantification.
- [STAR-Fusion/STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) - Uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads.
- [stemangiola/bioc_2020_tidytranscriptomics](https://github.com/stemangiola/bioc_2020_tidytranscriptomics) - A tidy transcriptomics introduction to RNA sequencing analyses.
- [stemangiola/bioc_2020](https://github.com/stemangiola/bioc_2020_tidytranscriptomics) - A tidy transcriptomics introduction to RNA sequencing analyses.
- [suhrig/arriba](https://github.com/suhrig/arriba) - Fast and accurate gene fusion detection from RNA-Seq data.

## Sequence feature utilities
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