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  • Rnaseqlib
    [[Category:Software]][[Category:Biology]][[Category:Phylogenetics]][[Category:RNA-Seq]] rnaseqlib is a simple, lightweight pipeline for RNA-Seq analysis.
    2 KB (247 words) - 15:15, 10 June 2022
  • Rascaf
    ...contigs within scaffolds and chromosomes. When Rascaf is run with multiple RNA-seq data sets, it first generates a set of connections for each set independent ...ng, L., Shankar, D. and Florea, L. "Rascaf: Improving Genome Assembly with RNA-seq Data", The Plant Genome, 2016. doi: 10.3835/plantgenome2016.03.0027.]
    3 KB (415 words) - 21:30, 21 August 2022
  • Circexplorer3
    [[Category:RNA-Seq]] ...lar and Linear RNA Expression Analysis from Ribosomal-RNA depleted (Ribo–) RNA-seq (CLEAR/CIRCexplorer3).
    2 KB (271 words) - 15:06, 18 January 2023
  • Ngscheckmate
    ...ividual. Our alignment-free module is fast (e.g., less than one minute for RNA-seq using a single core) and we recommend it for a quick initial quality check,
    3 KB (390 words) - 18:12, 27 May 2022
  • Rcorrector
    ...ector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. ...orea, L., Rcorrector: Efficient and accurate error correction for Illumina RNA-seq reads. GigaScience. 2015, 4:48.
    2 KB (282 words) - 13:58, 6 June 2022
  • STAR
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]] STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
    2 KB (291 words) - 16:01, 22 August 2022
  • RSeQC
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]] ...equence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq specific modules” investigate sequencing saturation status of both splici
    3 KB (328 words) - 17:48, 10 June 2022
  • Regtools
    [[Category:Software]][[Category:Biology]][[Category:RNA-Seq]][[Category:Genomics]] Regtools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
    2 KB (254 words) - 21:41, 21 August 2022
  • MATS
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]] ...ne between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events
    3 KB (332 words) - 18:25, 18 August 2022
  • Pyrpipe
    ...an be used on local computers or on HPC environments to manage analysis of RNA-Seq data. Users can use the easy-to-use APIs to popular bioinformatic tools pro
    3 KB (311 words) - 15:22, 16 March 2020
  • Sailfish
    ...tware]][[Category:Biology]][[Category:NGS]][[Category:Genomics]][[Category:RNA-Seq]] RNA-seq expression estimates need not take longer than a cup of coffee
    4 KB (482 words) - 22:02, 21 August 2022
  • SpliceGrapher
    SpliceGrapher is a Python package for creating splice graphs from RNA-Seq data, guided by gene models and EST data (when available). Starting with ve ...A. Ben-Hur. SpliceGrapher: Detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data. Genome Biology, Vol. 13, 2
    3 KB (318 words) - 21:24, 6 December 2019
  • IRFinder
    [[Category:Software]][[Category:Biology]][[Category:RNA-Seq]] Detecting intron retention from RNA-Seq experiments
    2 KB (244 words) - 14:59, 10 June 2022
  • EXpress
    transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding
    3 KB (383 words) - 18:53, 12 August 2022
  • MISO
    ...are]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]][[Category:RNA-Seq]] ...deling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a r
    3 KB (390 words) - 20:44, 18 August 2022
  • GFOLD
    [[Category:Software]][[Category:Biology]][[Category:RNA-Seq]] ...- Generalized fold change for ranking differentially expressed genes from RNA-seq data.
    3 KB (388 words) - 18:54, 10 June 2022
  • GenomicTools
    ...tware]][[Category:NGS]][[Category:Biology]][[Category:ChIP-Seq]][[Category:RNA-Seq]] ...r the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-seq. GenomicTools implements a variety of mathematical operations
    3 KB (385 words) - 18:58, 12 August 2022
  • Kallisto
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]] Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencin
    2 KB (278 words) - 16:13, 10 June 2022
  • VAST-TOOLS
    [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]] toolset for profiling alternative splicing events in RNA-Seq data.
    2 KB (264 words) - 17:26, 22 August 2022
  • PsiCLASS
    ...ions, PsiCLASS takes a multi-sample approach, simultaneously analyzing all RNA-seq data sets in an experiment. PsiCLASS is both a transcript assembler and a m ...-large collections of RNA-seq data, its accuracy is equally high for small RNA-seq data sets (2-10 samples) and is competitive to reference methods for single
    4 KB (480 words) - 15:00, 14 December 2022
  • 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
  • Ctk
    3 KB (297 words) - 16:53, 10 October 2022
  • 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
  • DeSALT
    alignment, deSALT is a fast and accurate RNA-seq long read alignment
    3 KB (350 words) - 14:38, 15 August 2022

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