Search results

• READemption
  READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed to process dRNA-Seq reads (as introduced
  3 KB (352 words) - 17:58, 1 June 2022
• Arriba
  Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefor
  3 KB (363 words) - 14:07, 1 April 2021
• Infernal
  3 KB (305 words) - 19:31, 24 August 2022
• TACO
  TACO: Multi-sample transcriptome assembly from RNA-Seq
  2 KB (234 words) - 18:53, 1 June 2022
• MELTING
  3 KB (306 words) - 19:50, 12 August 2022
• MAJIQ
  ...ether detect, quantify, and visualize local splicing variations (LSV) from RNA-Seq data.
  2 KB (247 words) - 14:59, 10 June 2022
• Hyb
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]]
  2 KB (247 words) - 15:07, 10 June 2022
• RnaQUAST
  ...are]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]][[Category:RNA-Seq]]
  2 KB (257 words) - 21:57, 21 August 2022
• DoGFinder
  ...package that identifies DoGs and quantifies their expression levels, from RNA-seq data.
  2 KB (252 words) - 21:58, 3 November 2020
• TEToolkit
  TEtranscripts takes RNA-seq (and similar data) and annotates reads to both genes & transposable element
  2 KB (259 words) - 20:46, 12 August 2022
• 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
• Isonclust2
  [[Category:RNA-Seq]]
  3 KB (303 words) - 15:23, 28 October 2022
• Stringtie
  StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It is primarily a genome-guided tran
  3 KB (301 words) - 20:45, 12 August 2022
• SOAPsplice
  sites from RNA-Seq. The tool performs better than the previous tools by
  3 KB (315 words) - 00:06, 22 August 2022
• CLIFinder
  ...ifically designed to identify potential LCTs from one or several oriented RNA-seq paired-end reads in the human genome.
  3 KB (308 words) - 21:11, 6 December 2019
• Necklace
  In species where the reference genome or annotation is incomplete, RNA-Seq analyses can benefit from performing a genome-guided and de novo assembly,
  3 KB (312 words) - 21:22, 6 December 2019
• EpiNano
  2 KB (241 words) - 18:35, 21 July 2022
• Hylite
  ...levels can technically be determined from next generation sequencing data (RNA-seq), but in practice, assigning reads to one homeolog over another is extremel
  3 KB (325 words) - 21:51, 24 February 2023
• Crossmapper
  ...be used for planning such kind of experimental setups as dual- or multiple RNA-seq (mainly for host-pathogen, symbiont and cohabitant interaction studies), me
  3 KB (326 words) - 17:40, 31 January 2022
• RiboPicker
  3 KB (377 words) - 21:50, 21 August 2022
• LIQA
  alternative splicing (DAS) events using long-read RNA-seq data. LIQA incorporates
  3 KB (319 words) - 20:03, 15 August 2022
• Alevin-fry
  ...ry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods 19, 316–322 (2022). https://doi.org/10.1038/s41592-022-
  3 KB (320 words) - 18:28, 9 February 2023
• Paralyzer
  3 KB (352 words) - 18:19, 27 May 2022
• BBMap
  BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffo
  3 KB (349 words) - 17:55, 10 June 2022
• QUAST
  ...are]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]][[Category:RNA-Seq]]
  3 KB (361 words) - 21:01, 21 August 2022
• Portcullis
  ...s stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that RNAseq mapping tools generate many invalid junction
  3 KB (343 words) - 19:18, 31 January 2022
• SpliceTrap
  ...ap is a statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. Splice
  3 KB (347 words) - 20:44, 12 August 2022
• Mireap
  2 KB (258 words) - 20:43, 18 August 2022
• Finder
  ...f. FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences.bioRxiv, page 2021.02.04.429837, 2 20
  3 KB (345 words) - 16:42, 15 August 2022
• Velocyto
  2 KB (275 words) - 00:33, 25 May 2023
• MiXCR
  ...umacher & Dmitriy M. Chudakov. "Antigen receptor repertoire profiling from RNA-seq data." Nature Biotechnology 35, 908–911 (2017)
  3 KB (340 words) - 21:22, 6 December 2019

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