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• Quantas
  Quantas: A pipeline to analyze alternative splicing using RNA-Seq
  2 KB (247 words) - 20:29, 12 August 2022
• Umi-tools
  ...Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
  2 KB (254 words) - 14:46, 4 September 2020
• Trans-ABySS
  ...eth.1517.html Robertson, G., et al. 2010. De novo assembly and analysis of RNA-seq data. Nature Methods 7, 909-912(2010)]
  2 KB (260 words) - 15:39, 10 June 2022
• CellRanger-DNA
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]][[Category:Genomics]]
  2 KB (263 words) - 13:25, 15 August 2022
• MiRge
  miRge is a logical, ultrafast, small RNA-seq solution to process samples in a highly multiplexed fashion, resulting in d
  2 KB (279 words) - 21:22, 6 December 2019
• TraCeR
  ...quences of rearranged and expressed T cell receptor genes from single-cell RNA-seq data. It then uses the TCR sequences to identify cells that have the same r
  2 KB (277 words) - 16:40, 22 August 2022
• CLIPper
  2 KB (277 words) - 13:44, 15 August 2022
• Erpin
  3 KB (377 words) - 21:21, 6 December 2019
• CellRanger-ATAC
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]]
  2 KB (281 words) - 13:25, 15 August 2022
• CellRanger-ARC
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]]
  3 KB (288 words) - 18:24, 12 August 2022
• Ctk
  3 KB (297 words) - 16:53, 10 October 2022
• Nanocompore
  3 KB (298 words) - 20:48, 10 May 2024
• Zagros
  2 KB (289 words) - 17:54, 22 August 2022
• IRAP
  iRAP is a flexible RNA-seq analysis pipeline that allows the user to select and apply their preferred
  2 KB (296 words) - 20:10, 24 August 2022
• Ciriquant
  ...omprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data
  2 KB (275 words) - 15:00, 30 March 2022
• ZUMIS
  zUMIs is a fast and flexible pipeline to process RNA-seq data with (or without) UMIs.
  2 KB (302 words) - 17:55, 22 August 2022
• FLASh
  .... They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
  2 KB (297 words) - 16:44, 15 August 2022
• CIMS
  3 KB (315 words) - 17:21, 10 June 2022
• ShapeMapper
  3 KB (387 words) - 21:24, 6 December 2019
• BRANCH
  Bao E, Jiang T, Girke T (2013). BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences. Bioinformatics: [http
  3 KB (309 words) - 13:09, 15 August 2022

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