CompcodeR CompcodeR— RNAseq information simulation, differential expression Examination and overall performance comparison of differential expression approaches.
qRNASeq script qRNASeq script. The qRNAseq Device may be used to correctly eradicate PCR duplicates from RNA-Seq information if Molecular Indexes™ or other stochastic labels have been applied through library prep.
interactions with the dataset. As soon as the Original Construct is entire, this operate will default to using the database for all potential classes. Crucial: - Every single R session should start out with a contact to readCufflinks to re-open up the link to your database.
Taverna Taverna. Taverna is undoubtedly an open source and domain-unbiased Workflow Management Technique – a suite of instruments accustomed to design and execute scientific workflows and support in silico experimentation.
STAR STAR is undoubtedly an ultrafast Software that employs "sequential optimum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching treatment", detects canonical, non-canonical splices junctions and chimeric-fusion sequences.
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BayesHammer BayesHammer. Bayesian clustering for error correction. We introduce several novel algorithms based on Hamming graphs and Bayesian subclustering within our new error correction Software BAYES HAMMER. Even though BAYES HAMMER was designed for single-mobile sequencing, we reveal that What's more, it increases on current error correction resources for multi-mobile sequencing data though Doing the job considerably quicker on real-life datasets.
Scotty Scotty Performs energy Evaluation to estimate the number of replicates and depth of sequencing required to phone differential expression.
SEECER seecer SEECER is often a sequencing error correction algorithm for RNA-seq data sets. It requires the raw examine sequences made by a next generation sequencing platform like devices from Illumina or here Roche.
FASTX FASTX Toolkit is usually a list of command line resources to govern reads in files FASTA or FASTQ format. These commands make achievable preprocess the files prior to mapping with tools like Bowtie.
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Sleuth Sleuth can be a program for Evaluation of RNA-Seq experiments for which transcript abundances have been quantified with kallisto.
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