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

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