All software used or developed by the ENCODE Consortium
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DESeq2 — sourceDifferential gene expression analysis based on the negative binomial distribution
Software type: quantification
CQN — sourceSoftware used to generate GC content and length normalized matrix
Software type: quantification
Salmon — sourceSoftware used to generate transcriptome quantifications
Software type: quantification
Tximport — sourceSoftware used to generate length scaled TPM matrix
Software type: quantification
Surrogate Variable Analysis — sourceThe sva package in Bioconductor contains functions for removing batch effects and other unwanted variation in high-throughput experiment.
Software type: other
Cuffdiff — sourceCuffdiff can be used to find significant changes in transcript expression, splicing, and promoter use.
Software type: quantification
Miso — sourceMISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples
Software type: quantification
rMATs — sourceMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.
Software type: quantification
DESeq — sourceDESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression.
Software type: quantification