Search results

• PureCLIP
  2 KB (285 words) - 21:24, 6 December 2019
• Circompara2
  ...etect, quantify, and correlate expression of linear and circular RNAs from RNA-seq data that combines multiple circRNA-detection methods. ...Stefania Bortoluzzi, Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2, Briefings in Bioinformatics, 2021;, bbab418, https://doi.
  2 KB (283 words) - 21:36, 1 April 2022
• SplAdder
  ...RNA-Seq alignment data. Briefly, the software takes a given annotation and RNA-Seq read alignments in standardized formats, transforms the annotation into a s
  3 KB (304 words) - 15:50, 22 August 2022
• CIRCexplorer
  [[Category:Software]][[Category:Biology]][[Category:RNA-Seq]]
  3 KB (308 words) - 18:29, 12 August 2022
• Trinity
  ...are]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]][[Category:RNA-Seq]] ...Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn
  4 KB (556 words) - 17:10, 22 August 2022
• Salmon
  [[Category:Software]][[Category:Biology]][[Category:RNA-Seq]] Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or d
  3 KB (305 words) - 19:29, 3 June 2022
• QAPA
  Analysis of alternative polyadenylation (APA) from RNA-seq data (human and mouse). QAPA consists of two main components: ...new method for the systematic analysis of alternative polyadenylation from RNA-seq data. Genome Biol. 19, 45.]
  3 KB (305 words) - 16:54, 15 January 2021
• CellRanger
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]] ...anger is a set of analysis pipelines that processes Chromium single cell 3 RNA-seq output to align reads, generate gene-cell matrices and perform clustering a
  2 KB (294 words) - 18:24, 12 August 2022
• Captus
  ...ta such as Genome Skimming, Hyb-Seq (Target Enrichment + Genome Skimming), RNA-seq, and Whole Genome Sequencing. The toolkit will also include a module for th
  3 KB (321 words) - 16:36, 16 November 2022
• Cufflinks
  ...ferential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts.
  2 KB (307 words) - 14:17, 15 August 2022
• Dapars
  DaPars(Dynamic analysis of Alternative PolyAdenylation from RNA-seq) ...er E.J., Li, W. 2014. Dynamic Analyses of Alternative Polyadenylation from RNA-Seq Reveal 3'-UTR Landscape Across 7 Tumor Types. Nature Communications, 5:5274
  3 KB (306 words) - 20:05, 23 March 2023
• Rnalysis
  Near-optimal probabilistic RNA-seq quantification. “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.”
  5 KB (648 words) - 16:12, 25 April 2023
• Bridger
  ...''de novo'' transcriptome assembler for RNA-Seq data. It expects as input RNA-Seq reads (single or paired) in fasta or fastq format, outputs all transcripts
  3 KB (341 words) - 13:14, 15 August 2022
• QualiMap
  *rnaseq - Evaluate RNA-seq alignment data *counts - Counts data analysis (further RNA-seq data evaluation)
  3 KB (326 words) - 19:32, 24 August 2022
• HOMER
  ...s data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing
  3 KB (330 words) - 18:19, 15 August 2022
• KisSplice
  KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome ...cent Lacroix*, KISSPLICE: de-novo calling alternative splicing events from RNA-seq data, BMC Bioinformatics 2012, 13(Suppl 6):S5]
  3 KB (359 words) - 19:33, 15 August 2022
• Rnaeditingindexer
  2 KB (239 words) - 22:53, 21 January 2024
• BinPacker
  ...single or paired) without using a reference. The software expects as input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcrip
  3 KB (365 words) - 12:53, 15 August 2022
• Tophat
  TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read
  3 KB (366 words) - 16:39, 22 August 2022
• TransDecoder
  sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome
  3 KB (371 words) - 16:54, 22 August 2022
• IGB
  ...r you can use to view and explore genomic data and annotations, especially RNA-Seq and ChIP-Seq data sets.
  2 KB (257 words) - 18:41, 15 August 2022
• Barrnap
  [[Category:Software]][[Category:Biology]][[Category:RNA-Seq]]
  3 KB (328 words) - 17:55, 10 June 2022
• SCRIPTURE
  Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The stati
  3 KB (302 words) - 20:36, 12 August 2022
• Magicblast
  ...taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This
  2 KB (304 words) - 16:29, 6 October 2022
• Olego
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]]
  3 KB (309 words) - 17:44, 19 August 2022
• ViennaRNA
  [[Category:Software]][[Category:Biology]][[Category:RNA-Seq]]
  3 KB (396 words) - 19:08, 10 June 2022
• Stampy
  ...recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain
  3 KB (327 words) - 20:45, 12 August 2022
• FEELnc
  ...ate long non-coding RNAs (lncRNAs) based on reconstructed transcripts from RNA-seq data (either with or without a reference genome). For a more general overvi
  3 KB (322 words) - 18:53, 10 July 2020
• BAM-matcher
  ...-genome-sequencing (WGS), whole-exome-sequencing (WES) and RNA-sequencing (RNA-seq) human data, but can also be customised to compare panel data or non-human
  3 KB (324 words) - 21:07, 6 December 2019
• RNAmmer
  [[Category:Software]][[Category:Biology]][[Category:RNA-Seq]]
  3 KB (328 words) - 17:35, 10 June 2022
• 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

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