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• Category:RNA-Seq
  28 members (0 subcategories, 0 files) - 15:28, 23 August 2022

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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

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